Trading_CatalogProductType Class Reference
| Inherits from | NSObject |
| Conforms to | PicoBindable |
| Declared in | Trading_CatalogProductType.h Trading_CatalogProductType.m |
Tasks
-
title
The title of the product. Always returned when Product is returned.
property -
detailsURL
Fully qualified URL for optional information about the product,
property
such as a movie’s description or film credits. This information
is hosted through the eBay Web site and it cannot be edited.
Portions of the content are protected by copyright.
Applications can include this URL as a link in product search results
so that end users can view additional descriptive details about
the product.
Note: You can use
the ProductMementoString parameter in this URL as the ProductID value in
GetSearchResults requests. This parameter is a colon-delimited
alphanumeric value. For an example of how to use this string,
see the GetProducts samples in the eBay Web Services guide. -
stockPhotoURL
Fully qualified URL for a stock image (if any) that is associated
property
with the eBay catalog product. The URL is for the image eBay
usually displays in product search results (usually 70px tall).
It may be helpful to calculate the dimensions of the photo
programmatically before displaying it. -
displayStockPhotos
If true, your application can attempt to display stock photos that
property
are returned. If false, your application should not attempt to display
any stock photos that are returned. This recommendation is useful for
catalog data related to products like coins, where stock photos are not
necessarily applicable or available. An application with a graphical
user interface can use this flag to determine
when to hide customized stock photo widgets. -
itemCount
Total number of listings on the specified eBay site that use
property
stock information from this catalog product. This value can be greater
than the number of listings returned in ItemArray. To retrieve more
listings, use GetSearchResults.
Only returned when you use ExternalProductID or ProductReferenceID
and you set IncludeItemArray to true. -
externalProductID
An ISBN, UPC, or EAN value that is associated with this
property
eBay catalog product (if any). These values are only returned
for products in “media” domains (Books, DVDs and Movies, Music, and
Video Games). Products in other domains don’t return this value
(even if a UPC is available in the Item Specifics.)
Please note that as of February 2007, GetProducts may temporarily return
two ExternalProductID nodes for ISBN for some sites (one with a 13-digit
value and one with a 10-digit value). This is a bug and it will be fixed in
an upcoming release. Instead, one ExternalProductID node will be returned
with an additional field. Do not code your application to expect multiple
ExternalProductID nodes to be returned for ISBN values on an ongoing basis. -
productReferenceID
The numeric ID for the eBay catalog product. After selecting a product
property
returned from a keyword query, pass this value in GetProducts to
retrieve more information about that product. -
attributeSetID
Numeric ID for the product’s domain (characteristic set).
property
When you use GetProducts by itself, this can be useful when
you want to group product results
by domain (e.g., all book products together).
For a mapping of attribute set IDs to names, see the
eBay Web Services guide. Alternatively, use GetCategory2CS
to retrieve the mappings periodically (e.g., once a day) and
store them locally. (We do not recommend using the product histogram,
for this purpose.) -
itemSpecifics
A list of attribute and value pairs that are included in the product's
property
pre-filled Item Specifics.
Also see ExternalProductID for ISBN, UPC, or MPN values, if applicable.
This is usually returned. (We are not aware of any cases in which this
node is not be returned. However, it may be safest to check for the
existence of this node.) -
reviewCount
The total number of reviews that are available for this product
property
on the eBay Web site. This can be greater than the number of
reviews returned by GetProducts. See ReviewDetails.Review.URL
for information about viewing more reviews. -
reviewDetails
The product’s most helpful reviews, if any.
property
The reviews are sorted by most helpful review (most votes) first.
Only returned when you pass in ExternalProductID or
ProductReferenceID and you set IncludeReviewDetails to true.
Up to 20 of the reviews are returned. If more reviews are available,
(that is, if ReviewCount is greater than 20), the user can look at
additional reviews on the eBay Web site.
See ReviewDetails.Review.URL for information about viewing more
reviews. -
productState
Indicates that the product has changed or will soon change (usually due to a migration
property
from one catalog to another catalog). Typically, this field is returned for up to 90
days for a given product. After that, the product either no longer returns this field
or the product is no longer returned (depending on the state change).
This data is primarily applicable to catalogs used by the US, Germany, Austria, and
Switzerland sites. Other sites may undergo catalog changes in the future. -
any
(public property)
property
Properties
any
(public property)
@property (nonatomic, retain) NSMutableArray *any
Discussion
(public property)
entry type : PicoAnyElement, wrapper for primitive anyelement
Declared In
Trading_CatalogProductType.h
attributeSetID
Numeric ID for the product’s domain (characteristic set).
When you use GetProducts by itself, this can be useful when
you want to group product results
by domain (e.g., all book products together).
For a mapping of attribute set IDs to names, see the
eBay Web Services guide. Alternatively, use GetCategory2CS
to retrieve the mappings periodically (e.g., once a day) and
store them locally. (We do not recommend using the product histogram,
for this purpose.)
@property (nonatomic, retain) NSNumber *attributeSetID
Discussion
Numeric ID for the product’s domain (characteristic set).
When you use GetProducts by itself, this can be useful when
you want to group product results
by domain (e.g., all book products together).
For a mapping of attribute set IDs to names, see the
eBay Web Services guide. Alternatively, use GetCategory2CS
to retrieve the mappings periodically (e.g., once a day) and
store them locally. (We do not recommend using the product histogram,
for this purpose.)
type : NSNumber, wrapper for primitive int
Declared In
Trading_CatalogProductType.h
detailsURL
Fully qualified URL for optional information about the product,
such as a movie’s description or film credits. This information
is hosted through the eBay Web site and it cannot be edited.
Portions of the content are protected by copyright.
Applications can include this URL as a link in product search results
so that end users can view additional descriptive details about
the product.
Note: You can use
the ProductMementoString parameter in this URL as the ProductID value in
GetSearchResults requests. This parameter is a colon-delimited
alphanumeric value. For an example of how to use this string,
see the GetProducts samples in the eBay Web Services guide.
@property (nonatomic, retain) NSString *detailsURL
Discussion
Fully qualified URL for optional information about the product,
such as a movie’s description or film credits. This information
is hosted through the eBay Web site and it cannot be edited.
Portions of the content are protected by copyright.
Applications can include this URL as a link in product search results
so that end users can view additional descriptive details about
the product.
Note: You can use
the ProductMementoString parameter in this URL as the ProductID value in
GetSearchResults requests. This parameter is a colon-delimited
alphanumeric value. For an example of how to use this string,
see the GetProducts samples in the eBay Web Services guide.
type : NSString, wrapper for primitive string
Declared In
Trading_CatalogProductType.h
displayStockPhotos
If true, your application can attempt to display stock photos that
are returned. If false, your application should not attempt to display
any stock photos that are returned. This recommendation is useful for
catalog data related to products like coins, where stock photos are not
necessarily applicable or available. An application with a graphical
user interface can use this flag to determine
when to hide customized stock photo widgets.
@property (nonatomic, retain) NSNumber *displayStockPhotos
Discussion
If true, your application can attempt to display stock photos that
are returned. If false, your application should not attempt to display
any stock photos that are returned. This recommendation is useful for
catalog data related to products like coins, where stock photos are not
necessarily applicable or available. An application with a graphical
user interface can use this flag to determine
when to hide customized stock photo widgets.
type : NSNumber, wrapper for primitive bool
Declared In
Trading_CatalogProductType.h
externalProductID
An ISBN, UPC, or EAN value that is associated with this
eBay catalog product (if any). These values are only returned
for products in “media” domains (Books, DVDs and Movies, Music, and
Video Games). Products in other domains don’t return this value
(even if a UPC is available in the Item Specifics.)
Please note that as of February 2007, GetProducts may temporarily return
two ExternalProductID nodes for ISBN for some sites (one with a 13-digit
value and one with a 10-digit value). This is a bug and it will be fixed in
an upcoming release. Instead, one ExternalProductID node will be returned
with an additional field. Do not code your application to expect multiple
ExternalProductID nodes to be returned for ISBN values on an ongoing basis.
@property (nonatomic, retain) Trading_ExternalProductIDType *externalProductID
Discussion
An ISBN, UPC, or EAN value that is associated with this
eBay catalog product (if any). These values are only returned
for products in “media” domains (Books, DVDs and Movies, Music, and
Video Games). Products in other domains don’t return this value
(even if a UPC is available in the Item Specifics.)
Please note that as of February 2007, GetProducts may temporarily return
two ExternalProductID nodes for ISBN for some sites (one with a 13-digit
value and one with a 10-digit value). This is a bug and it will be fixed in
an upcoming release. Instead, one ExternalProductID node will be returned
with an additional field. Do not code your application to expect multiple
ExternalProductID nodes to be returned for ISBN values on an ongoing basis.
type : class Trading_ExternalProductIDType
Declared In
Trading_CatalogProductType.h
itemCount
Total number of listings on the specified eBay site that use
stock information from this catalog product. This value can be greater
than the number of listings returned in ItemArray. To retrieve more
listings, use GetSearchResults.
Only returned when you use ExternalProductID or ProductReferenceID
and you set IncludeItemArray to true.
@property (nonatomic, retain) NSNumber *itemCount
Discussion
Total number of listings on the specified eBay site that use
stock information from this catalog product. This value can be greater
than the number of listings returned in ItemArray. To retrieve more
listings, use GetSearchResults.
Only returned when you use ExternalProductID or ProductReferenceID
and you set IncludeItemArray to true.
type : NSNumber, wrapper for primitive int
Declared In
Trading_CatalogProductType.h
itemSpecifics
A list of attribute and value pairs that are included in the product's
pre-filled Item Specifics.
Also see ExternalProductID for ISBN, UPC, or MPN values, if applicable.
This is usually returned. (We are not aware of any cases in which this
node is not be returned. However, it may be safest to check for the
existence of this node.)
@property (nonatomic, retain) Trading_NameValueListArrayType *itemSpecifics
Discussion
A list of attribute and value pairs that are included in the product's
pre-filled Item Specifics.
Also see ExternalProductID for ISBN, UPC, or MPN values, if applicable.
This is usually returned. (We are not aware of any cases in which this
node is not be returned. However, it may be safest to check for the
existence of this node.)
type : class Trading_NameValueListArrayType
Declared In
Trading_CatalogProductType.h
productReferenceID
The numeric ID for the eBay catalog product. After selecting a product
returned from a keyword query, pass this value in GetProducts to
retrieve more information about that product.
@property (nonatomic, retain) NSNumber *productReferenceID
Discussion
The numeric ID for the eBay catalog product. After selecting a product
returned from a keyword query, pass this value in GetProducts to
retrieve more information about that product.
type : NSNumber, wrapper for primitive long
Declared In
Trading_CatalogProductType.h
productState
Indicates that the product has changed or will soon change (usually due to a migration
from one catalog to another catalog). Typically, this field is returned for up to 90
days for a given product. After that, the product either no longer returns this field
or the product is no longer returned (depending on the state change).
This data is primarily applicable to catalogs used by the US, Germany, Austria, and
Switzerland sites. Other sites may undergo catalog changes in the future.
@property (nonatomic, retain) NSString *productState
Discussion
Indicates that the product has changed or will soon change (usually due to a migration
from one catalog to another catalog). Typically, this field is returned for up to 90
days for a given product. After that, the product either no longer returns this field
or the product is no longer returned (depending on the state change).
This data is primarily applicable to catalogs used by the US, Germany, Austria, and
Switzerland sites. Other sites may undergo catalog changes in the future.
type: string constant in Trading_ProductStateCodeType.h
Declared In
Trading_CatalogProductType.h
reviewCount
The total number of reviews that are available for this product
on the eBay Web site. This can be greater than the number of
reviews returned by GetProducts. See ReviewDetails.Review.URL
for information about viewing more reviews.
@property (nonatomic, retain) NSNumber *reviewCount
Discussion
The total number of reviews that are available for this product
on the eBay Web site. This can be greater than the number of
reviews returned by GetProducts. See ReviewDetails.Review.URL
for information about viewing more reviews.
type : NSNumber, wrapper for primitive int
Declared In
Trading_CatalogProductType.h
reviewDetails
The product’s most helpful reviews, if any.
The reviews are sorted by most helpful review (most votes) first.
Only returned when you pass in ExternalProductID or
ProductReferenceID and you set IncludeReviewDetails to true.
Up to 20 of the reviews are returned. If more reviews are available,
(that is, if ReviewCount is greater than 20), the user can look at
additional reviews on the eBay Web site.
See ReviewDetails.Review.URL for information about viewing more
reviews.
@property (nonatomic, retain) Trading_ReviewDetailsType *reviewDetails
Discussion
The product’s most helpful reviews, if any.
The reviews are sorted by most helpful review (most votes) first.
Only returned when you pass in ExternalProductID or
ProductReferenceID and you set IncludeReviewDetails to true.
Up to 20 of the reviews are returned. If more reviews are available,
(that is, if ReviewCount is greater than 20), the user can look at
additional reviews on the eBay Web site.
See ReviewDetails.Review.URL for information about viewing more
reviews.
type : class Trading_ReviewDetailsType
Declared In
Trading_CatalogProductType.h
stockPhotoURL
Fully qualified URL for a stock image (if any) that is associated
with the eBay catalog product. The URL is for the image eBay
usually displays in product search results (usually 70px tall).
It may be helpful to calculate the dimensions of the photo
programmatically before displaying it.
@property (nonatomic, retain) NSString *stockPhotoURL
Discussion
Fully qualified URL for a stock image (if any) that is associated
with the eBay catalog product. The URL is for the image eBay
usually displays in product search results (usually 70px tall).
It may be helpful to calculate the dimensions of the photo
programmatically before displaying it.
type : NSString, wrapper for primitive string
Declared In
Trading_CatalogProductType.h


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Three minds with the same eccentric idea, The Collective Café was created. The Collective Café wanted to create more than just a place to grab a cup of coffee but a space for a community of people to enjoy coffee that they learned to brew themselves.
The Collective Cafe started off in a small location in Surrey B.C and is now opening it's 2nd location in Downtown Vancouver!
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.


This page contains all the digits of
π
in hexadecimal.
Q: Really all of them?
A: Yes, if your machine has enough memory.
Q: Are they correct?
A: Yes,
check here
.
3.
.....


Origami Intructions and Diagrams
Step by Step diagrams are probably the most popular and easiest to follow way to show how to fold things out of paper.
Trying to find good origrami Intructions on the Internet can be a lot of work though. To help your search we've put
together the largest database of free origami diagrams anywhere on the Internet.


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Help on package cinemasqlpy:
NAME cinemasqlpy
PACKAGE CONTENTS a
DATA all = ['a']
FILE /home/woodring/conda3/envs/test/lib/python3.5/site-packages/cinemasqlpy/init.py


Note: This form is a test, it does not record any information. TESTING ONLY!!
Please enter your name
Please enter your Age
Select one or more from list
What is your fav colour? Select one or more snacks from the list
What do you like doing?
Tell me what your best experience in life is


safegraph_aws.Rd
This is a thin wrapper for aws.s3::s3sync
that will aim you at the right directory to synchronize.
safegraph_aws( path = ".", dataset, bucket_only = FALSE, base_url = "s3.wasabisys.com", key, secret, region = "", prefix = "", prefix_is_dir = FALSE, max_print = 1, ... )
| path | The local directory to synchronize. |
|---|---|
| dataset | The SafeGraph bucket to get from. Can be "weekly" (OLD VERSION), "weekly-new" (new method since December 2020), "weekly-backfill" (the new method for times before December 2020), "monthly" (OLD VERSION, but also includes the backfill data for the new version), "monthly-backfill" (method since Dec 2020), "distancing", "core" (before Nov 2020), "core-new" (Nov 2020 or later), "geo-supplement" or, to get the baseline bucket, "none". v2 versions always selected. |
| bucket_only | Instead of doing an |
| base_url | The base URL to pull the data from. |
| key | A character string containing an AWS Access Key ID. |
| secret | A character string containing an AWS Secret Access Key. |
| region | A character string containing the AWS region. |
| prefix | Leading part of the objects in the bucket must have this prefix. For example, to download social distancing data only from 2020, set this to "2020/". |
| prefix_is_dir | If |
| max_print | Temporarily set |
| ... | Additional parameters to be sent to |
This function doesn't add too much, but it does make the default behavior you probably want a bit easier. If you plan to specify the aws.s3::s3sync
"bucket" option yourself, this function is largely useless.
See catalog.safegraph.io for more description of the various buckets.
if (FALSE) { # Download all the recent weekly-patterns files to the working directory safegraph_aws(dataset = 'weekly-new', key = 'MYINFO', secret = 'MYOTHERINFO') }


Do you want to buy the game?
If you want to support the devs of Starbound, you can buy it here! (Or just visit their homepage)
The Starbound Mod Manager enables users to handle multiple mod lists easily. (works with Steam!). No experience needed!
This application is in no way associated with Starbound and their creators Chucklefish! It was created by me to simplify the tedious task of managing many different mods for the game.
Hey, I am the creator of the StarboundModManager! You can click on my profile image to visit my Github accout, where I create even more stuff.
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A diary from Greenbrier County, West Virginia, this day in 1897:
Today I murdered my wife. I mashed her windpipe and broke her neck, which might seem an overreaction to the fact that she had not cooked any meat for my dinner, but then, as my first wife would tell you, I am a cruel and horrible and violent man. My second wife would probably say the same, had she not died in mysterious circumstances shortly after our marriage. Zona, who I killed today, was my third wife. I hope to have seven eventually.
I won't get a chance to marry a further four wives if I am hanged or imprisoned for murder. So I took various steps to cover my tracks. I laid Zona out on the bed and dressed her in a high-necked dress with a stiff collar, and placed a veil over her face. When Dr Knapp arrived to examine the corpse, I sobbed and wailed and cradled Zona's head in my hands. That did the trick, and he did not inspect her too closely, noting that death was due to “everlasting faint”.
So everything went according to plan and I seem to be in the clear, free to find a fourth wife to terrorise and/or kill. The worst that could happen is that Zona might appear as a ghost, to her grieving mother, and spill the beans, and prove that I broke her neck by rotating her ghostly head in a full circle atop her ghostly body. But even if she does, repeatedly, over four nights, and Zona's mother goes babbling her tale, an American court of law in the enlightened 1890s is not going to accept the testimony of a ghost. Is it?


---
layout: default
title: TL;DR / Features
---
TL;DR
Perfect library for adding search, sort, filters and flexibility to tables, lists and various HTML elements. Built to be invisible and work on existing HTML.
Core idea
- Simple and invisible
- Easy to apply to existing HTML
- No dependencies
- Fast
- Tiny (5KB minified&gzip)
- Handle thousands of items
Features
- Works both lists, tables and almost anything else. E.g.

,

,

, etc.
- Search Read more ›
- Sort Read more ›
- Filter Read more ›
- Simple templating system that adds possibility to add, edit, remove items Read more ›
- Plugins Read more ›
- Support for Chrome, Safari, Firefox, IE6+
Used by


I enjoy people; either working together on a common goal/activity or just being open and available for peer coaching and mentorship. I have a thirst for knowledge and a quick ability to learn. I leverage great communication and analytical skills with attention to detail to ensure warm hand offs and speedy resolutions.
Prepare repair orders, enter them into the database system and close the orders through CDK Dealer software. Answer technical questions about vehicle problems, warranties, services, and repairs. Perform administrative duties such as opening and closing invoices, rental vehicle management, contacting customers for accessories and dealership vendor appointments. Handle orders and requests for information efficiently via telephone and over the counter from customers and technicians. In conjunction with the service department, solicit sales and suggest selling of service-related parts. Answer questions and assist customers and technicians in identifying and obtaining required parts.
Processed large volumes of daily access requests for both Windows and Applications utilized by the whole RBC enterprise ~70,000+ RBC employees via HP Service Manager 9. Mainly responsible for administering service accounts/mailboxes through NetIQ DRA,Active Directory, Microsoft Exchange Server, Auto SAB and Archer Systems. Identified gaps in adminis-trative processes; followed up with team leaders to provide solutions and work together to ensure quick resolutions and work together to ensure process improvements.
Digital cheque processing and imaging project. Managed the release life cycle which included scheduling, coordinating and the management of release across the enterprise for multiple platforms and applications. Developed and executed implementation and deployment plans. Coordinated with application developers, QA analyst, DBAs, product managers and program managers to maintain consistent configuration states across all environments. Enforced configuration policies and process documentation in order to maintain code integrity through the development life cycle. Performed end to end testing after deployments to ensure completion.
Assisted RBC recruitment team in promoting RBC events and co-op/new grad opportunities. Hosted events to promote RBC on campus. Networked with students on campus and acted as the point of contact for any RBC career related questions. Participated in monthly on-call student ambassador meet-ings with the manger and provided feedback to improve the program.
Represent RBC by being a role model for others in the community. Interacted with the community members to know their interests and help enhance their co-op experience by promoting events, challenges and tools supporting the student experience (e.g.:RBC Connect and Backpack). Engaged by planning socials for the community members. Actively shared feedback with the Community Manager for improvements in the student program.
Collected personal e-waste items at designated collection locations GEEP ensured all qualifying items were properly recycled with emphasis on the responsible disposal of any hazardous materials.


This library lets you store any data inside any image and retrieve it later. It can be a text, a script or another image.
npm-package
image before the data is merged
function hello(name = 'Mario') { alert('Hello '+name+'!'); }
merge data
show code on image
image after the data is merged
recovery data


This website itself is a work in progress, to see the html code I wrote you can "View page source" or "Inspect".
Below you can find a link to the basic elements I include in my code and how to learn how I did it.


Mix v1.3.4 Mix.Tasks.Compile.App
Writes an .app file.
An .app
file is a file containing Erlang terms that defines
your application. Mix automatically generates this file based on
your mix.exs
configuration. You can learn more about OTP
applications by seeing the documentation for the Application
module.
In order to generate the .app
file, Mix expects your application
to have both :app
and :version
keys. Furthermore, you can
configure the generated application by defining an application
function in your mix.exs
with the following options:
:applications
- all applications your application depends on at runtime. For example, if your application depends on Erlang’s:crypto
, it needs to be added to this list. Most of your dependencies must be added as well (unless they’re a development or test dependency). Mix and other tools use this list in order to properly boot your application dependencies before starting the application itself.:registered
- the name of all registered processes in the application. If your application defines a local GenServer with nameMyServer
, it is recommended to addMyServer
to this list. It is mostly useful to detect conflicts between applications that register the same names.:mod
- specify a module to invoke when the application is started, it must be in the format{Mod, args}
where args is often an empty list. The module specified here must implement the callbacks defined by theApplication
module.:env
- default values for the application environment. The application environment is one of the most common ways to configure applications.
Let’s see an example application
function:
def application do
[mod: {MyApp, []},
env: [default: :value],
applications: [:crypto]]
end
Besides the options above, .app
files also expects other
options like :modules
and :vsn
, but those are automatically
filled by Mix.
Command line options
--force
- forces compilation regardless of modification times
Summary
Functions
Callback implementation for Mix.Task.run/1
Functions
Callback implementation for Mix.Task.run/1
.


| Synonym | Reference | Specificity |
| H2B | Exact | |
| histone H2B | Exact |
| Identifier | Name | Relation |
| HGNC:13954 | H2BC12 | isa |
| HGNC:4761 | H2BC11 | isa |
| HGNC:20516 | H2BC20P | isa |
| HGNC:27252 | H2BW1 | isa |
| HGNC:4760 | H2BC21 | isa |
| HGNC:27867 | H2BW2 | isa |
| HGNC:4749 | H2BC15 | isa |
| HGNC:24700 | H2BC18 | isa |
| HGNC:4755 | H2BC9 | isa |
| HGNC:4762 | H2BC12L | isa |
| HGNC:4748 | H2BC13 | isa |
| HGNC:20514 | H2BU1 | isa |
| HGNC:4750 | H2BC14 | isa |
| HGNC:4751 | H2BC3 | isa |
| HGNC:18730 | H2BC1 | isa |
| HGNC:20517 | H2BC19P | isa |
| HGNC:4758 | H2BC17 | isa |
| UP:P62807 | H2BC4 | isa |
| HGNC:4747 | H2BC5 | isa |
| Relation | Identifier | Name |
| isa | FPLX:Histone | Histone |


Welcome to **SeqPlots**
=======================
> An interactive tool for visualizing track signals and sequence motif
> densities along genomic features using average plots and heatmaps.
![Examples of Seq Plots interfce and outputs](img/01_01.png)
Summary
-------
SeqPlots is a web browser tool for plotting average track signals (e.g.
read coverage) and sequence motif densities over user specified genomic
features. The data can be visualized in linear plots with error
estimates or as series of heatmaps that can be sorted and clustered. The
software can be run locally on a desktop or deployed on a server and
allows easy data sharing. SeqPlots pre-calculates and stores binary
result matrices, allowing rapid plot generation. Plots can also be run
in batch.
Availability
------------
SeqPlots is primarily distributed as R package available on platforms
and operating systems supported by R project. Standalone SeqPlot bundle,
combing R and all required packages, is available as for Mac OS X (10.6
or higher). SeqPlots can also be deployed on a server using free and
open sourced (GPL licensed) Shiny Server
(https://github.com/rstudio/shiny-server), making it available for
multiple clients. To deploy server version, clone the core\_master
branch of SeqPlots repository into your Shiny Server application
directory.
- [SeqPlots Bioconductor R
package](http://www.bioconductor.org/packages/release/bioc/html/seqplots.html)
- [SeqPlots OSX App](https://github.com/Przemol/seqplots/_osx/releases/latest)
Key features
------------
- Easy to use web interface (R or shell expertise not required)
- Web server or desktop versions
- Generates publication quality plots out of the box
- Plots average signals or heatmaps
- Accepts Wiggle, BedGraph, BigWiggle, and GFF and BED formats
- Calculates motif density from reference genome packages
- Tracks and features are searchable and old calculations stored
- Converts tracks to binary BigWiggle format for rapid data extraction
and efficient storage
- Implemented using Shiny R framework providing internet browser
reactive GUI and session based connectivity (websocets)
References
----------
**R project and Bioconductor**
- R Core Team (2014). R: A language and environment for statistical
computing. R Foundation for Statistical Computing, Vienna, Austria.
URL http://www.R-project.org/.
- Bioconductor: Open software development for computational biology
and bioinformatics R. Gentleman, V. J. Carey, D. M. Bates,
B.Bolstad, M.Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, and
others 2004, Genome Biology, Vol. 5, R80. URL
http://www.bioconductor.org/.
- RStudio and Inc. (2014). shiny: Web Application Framework for R. R
package version 0.10.1. http://shiny.rstudio.com/
- **Other CRAN packages:** digest, DBI,RSQLite, RJSONIO, plotrix,
fields, grid, kohonen, Cairo and parallel
- **Bioconductor packages:** IRanges, BSgenome, Rsamtools,
rtracklayer, GenomicRanges and Biostrings
**JavaScript and CSS**
- jQuery framework - http://jquery.com
- Bootstrap - http://getbootstrap.com
- DataTables, Table plug-in for jQuery - http://www.datatables.net
- jQuery File Upload Plugin -
https://github.com/blueimp/jQuery-File-Upload
- jQuery throttle -
http://benalman.com/projects/jquery-throttle-debounce-plugin/
- jQuery Cookie Plugin - https://github.com/carhartl/jquery-cookie
- Modernizer JS library - http://modernizr.com
- JavaScript Templates -
https://github.com/blueimp/JavaScript-Templates
- JavaScript Color Picker - http://jscolor.com
- md5-js - https://github.com/wbond/md5-js
- Font Awesome - http://fortawesome.github.io/Font-Awesome
- Google Fonts - https://www.google.com/fonts
- jQuery user interface - http://jqueryui.com (documentation)
- jquery.tocify.js: jQuery Table of Contents -
https://github.com/gfranko/jquery.tocify.js (documentation)
- Strapdown https://github.com/arturadib/strapdown (documentation)
- Bootswatch themes - http://bootswatch.com (documentation)
- google-code-prettify -
https://code.google.com/p/google-code-prettify (documentation)
- marked - https://github.com/chjj/marked (documentation)
**Important conceptual contribution to the project**
- Liu T, Ortiz J, Taing L, Meyer C, Lee B, Zhang Y, Shin H, Wong S, Ma
J, Lei Y, et al. 2011. [Cistrome: an integrative platform for
transcriptional regulation
studies.](http://www.ncbi.nlm.nih.gov/pubmed/21859476) Genome
Biology 12: R83.
- Thomas Williams, Colin Kelley and others (2010). Gnuplot 4.4: an
interactive plotting program. URL http://www.R-project.org/.
- Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H.,
Zahler, A.M. and Haussler, a. D. (2002). [The Human Genome Browser
at UCSC](http://www.ncbi.nlm.nih.gov/pubmed/12045153). Genome
Research. 12:996–1006.
- Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. (2010).
[BigWig and BigBed: enabling browsing of large distributed
datasets.](http://www.ncbi.nlm.nih.gov/pubmed/20639541)
Bioinformatics. 1;26(17):2204-7
- Nicol, J.W., Helt, G.A., Blanchard, S.G., Raja, A. and Loraine, A.E.
(2009). [The Integrated Genome Browser: free software for
distribution and exploration of genome-scale
datasets.](http://www.ncbi.nlm.nih.gov/pubmed/19654113)
Bioinformatics (Oxford, England). 25:2730–1.
- Thorvaldsdóttir, H., Robinson, J.T. and Mesirov, J.P. (2012).
[Integrative Genomics Viewer (IGV): high-performance genomics data
visualization and
exploration.](http://www.ncbi.nlm.nih.gov/pubmed/22517427) Briefings
in bioinformatics. bbs017
**Server deployment**
- Shiny Server - https://github.com/rstudio/shiny-server
- ShinyApps - https://github.com/rstudio/shinyapps
**Publications containing figures made by SeqPlots**
- Chen RA, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J.
[Extreme HOT regions are CpG-dense promoters in C. elegans and
humans.](http://www.ncbi.nlm.nih.gov/pubmed/24653213) Genome Res
24(7):1138-1146 Jul 2014
Quick start guide
=================
1. Start the SeqPlots. Refer to installation guides for platform
specific information. After successful initiation the web interface
should automatically open in your default web browser. If you are
web server user just navigate your browser to server address.
![The SeqPlots interface in web
browser](img/01_QuickStart/01_QuickStart_01.png)
2. Upload some feature (BED or GFF) and track (BigWig or WIG) files.
They can be gzip compressed (e.g. file1.bed.gz). Press green "Add
files..." button or just drag and drop files into the window. The
ready to upload files will show up in upload window, where you
select user name, reference genome and optionally add some comments.
![File upload panel](img/01_QuickStart/01_QuickStart_02.png)
3. When all is done press blue "Start upload" button. After upload and
processing is done the green "SUCCESS" label should show. It means
that file is on the registered and ready to use. Occasionally the
file might be mot formatted properly or chromosome names might not
agree with reference genome. In such case a verbose error will
window appears and file as labeled as "ERROR". For further
information please refer to **Explanations** chapter.
![File upload progress
infoermation](img/01_QuickStart/01_QuickStart_03.png)
4. Dismiss upload window and press blue "New plot set" button on side
panel. This will bring up file management window. In file management
window select at least one file from "Features" tab and either one
or more file from "Tracks" file or sequence motif(s). The sequence
motifs and tracks can be processed and plotted together.
![File management panel](img/01_QuickStart/01_QuickStart_04.png)
5. When you decided which files/motifs to plot it is time to set up the
processing options. You can find these in the button of plotting
window. For first plot you should do just fine with default options.
![Plot set calculation
options](img/01_QuickStart/01_QuickStart_05.png)
6. After options are set up press blue "Run calculation" button. This
will dismiss the file management window and show processing message.
Here you can observe the progress of the task and optionally cancel
it if no longer required or you forgot to add some very important
file to the plot-set (cancel available only in multi process mode).
![Plot set calculation progress
window](img/01_QuickStart/01_QuickStart_06.png)
7. After some time the calculation will finish (fingers crossed,
without the error) and you will be able to see plot set array. In
here you can choose which feature-track or feature-motif pairs to
plot. Choose one or more checkboxes and press grey "Line plot"
button (or hit RETURN from your keyboard). You can also check
"Reactive plotting" checkbook in the bottom of "Batch operations and
setup" tab - it will automatically apply changes to plots as soon as
you changed any plot-related option.
![The plot selection grid](img/01_QuickStart/01_QuickStart_07.png)
8. Congratulation! Your First plot is complete, you can see the preview
of it on the side panel.
![The plot preview panel](img/01_QuickStart/01_QuickStart_08.png)
9. You are able to set up labels, titles, font sizes, legends and many
more on side panel tabs, take a look at **Plotting**
chapter.
![Plot settings tabs](img/01_QuickStart/01_QuickStart_09.png)
10. By clicking the plot preview you can enlarge it for better view.
When everything is ready you can get the plot as PDF by clicking
green "Line plot" button just on the top of side panel.
![Average plot example](img/01_QuickStart/01_QuickStart_10.png)
11. You can also visualize the signal as a heatmap. Please note that
heatmap plotting is possible only for single feature file or files
containing exactly the same number of genomic ranges (which will
become the rows of heat map). For heatmap you can choose to sort
and/or cluster it using k-means.
![Heatmap settings tab](img/01_QuickStart/01_QuickStart_11.png)
12. Similarly to line plot you can grab the heatmap PDF using 'Heatmap'
button just on the top of side panel. Just attached to it, there is
small button allowing you to get cluster definitions.
![Heatmap example](img/01_QuickStart/01_QuickStart_12.png)
Installation: Mac OS X app
==========================
> The Mac OS X bundle is an easy way to use SeqPlots for Mac OS X users.
> It contains all R binaries and packages that SeqPlots depends on.
> Additionally, the reference sequences for *Caenorhabditis elegans* is
> included. The sequences for other popular model organisms can be
> downloaded using a graphical user interface.
**System requirements**
- Mac OS X Snow Leopard (10.6) or higher
- Xquartz package for OS X 10.8 (Mountain Lion) and above:
http://xquartz.macosforge.org/landing/
> More info: http://support.apple.com/en-us/HT201341
Installation
------------
1. Downaload the installation disk image from
https://github.com/Przemol/seqplots/_osx/releases/latest
2. Double-click on DMG file to mount the image or unzip the contents of
ZIP archive
3. Drag and drop SeqPlots.app to applications
> ![DMG image mounted in OS X](img/03_01.png)
Usage
-----
After starting SeqPlots the welcome screen displays the software
version, the currently installed genomes and the data folder location.
> ![SeqPlots Mac OS X bindle - the welcome screen](img/03_02.png)
This screen allows you to set up following options:
- Change your data location folder (by default your home directory
will be used)
- Install new genomes (requires internet connection). The correct
genome packages need to be installed before before uploading files
for plotting. A full list of supported genomes is available here:
http://www.bioconductor.org/packages/release/BiocViews.html\#\_\_\_BSgenome
> ![Genomic packages installer window](img/03_03.png)
Press the **`START`** button to initiate SeqPlots. If initiation was
successful the user interface should open in your default web browser.
For further usage please refer to **Quick start guide** or
specific chapters of this documentation.
The window in the background allows you to assess if SeqPlots is running
properly and exit the application at any moment.
> ![SeqPlots Mac OS X bindle - the diagnostic window](img/03_04.png)
The "moving" animation progress bar indicates that SeqPlots is running.
Press "Cancel" to stop it. Pressing "Details" will reveal a small text
window that displays diagnostic and error messages.
Package content
---------------
- Platypus (http://www.sveinbjorn.org/platypus) wrapper
- R (http://www.r-project.org/) branch 3.1 for Snow leopard
(http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86\_64.tar.gz)
- SeqPlots dependency packages (including Shiny, rtracklayer and
BSgenome)
- Full genome sequences for Caenorhabditis elegans (UCSC version ce10)
- BSgenome.Celegans.UCSC.ce10 R package
- SeqPlots package
Installation: R package
=======================
> The R package will run SeqPlots locally on desktop computers running
> Windows or Linux operating systems. The R package is also recommended
> for R users running Mac OS X machines.
**System requirements:**
- [R 3.1 or higher](http://www.r-project.org/)
Installation
------------
Install seqplots from from Bioconductor:
`source("http://bioconductor.org/biocLite.R") biocLite("seqplots")`
To use GitHub development version (in order to solve dependencies
install from Bioconductor first):
`if (!require("devtools")) install.packages("devtools") devtools::install_github('przemol/seqplots', build_vignettes=FALSE)`
Usage
-----
**To start web browser GUI:**
`library(seqplots) run()`
After a successful initiation the user interface will be opened in your
default web browser. For further usage please refer to
**Quick start guide** or specific chapters.
The `seqplots` function accepts "root" argument, which allows to change
the data location folder (by default your home directory will be used),
e.g.:
`run(root='/path/to/data/location')`
**To start with R scripting mode:**
`?getPlotSetArry`
### Additional genome packages
Genomic packages can be installed using standard bioconductor installer
(Internet connection required). For example, to instal human reference
genome (hg19):
`source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Hsapiens.UCSC.hg19")`
Genome packages are required before uploading files for plotting. Full
list of supported genomes is avilable here:
http://www.bioconductor.org/packages/release/BiocViews.html\#\_\_\_BSgenome
Installation: Deployment on the server
======================================
> The server version allows the sharing of signal and feature files by a
> group of users and for remote calculation and file storage. This is
> the ideal method for providing a shared SeqPlots service to a group.
**System requirements:**
- R 3.1 or higher
- Shiny Server 1.0 or higher
Installation
------------
1\. Install and configure the Shiny Server by following the instructions
on https://github.com/rstudio/shiny-server
2\. Install SeqPlots R package and dependences by following the
instruction in **Installation: R package**.
3\. Copy SeqPlots files to Shiny Server application folder:
`{bash eval=FALSE} cp -r $(Rscript -e "cat(system.file('seqplots', package='seqplots'))") /srv/shiny-server/`
4\. Set up SeqPlots **data location** by running from R:
`seqplots(root='/path/to/data/location')`
5\. Edit first line of `/srv/shiny-server/shiny/server_config.R`, so the
environment variable `root` matches the **data location**; for example:
`Sys.setenv('root'='/var/shiny-server/DATA')`
Usage
-----
After successful installation the SeqPlost web GUI will be available at
`your_server_name:3838/seqplots/`.
For further usage please refer to **Quick start guide** or
specific chapters.
### Additional genome packages
Genomic packages can be installed using standard bioconductor installer
(Internet connection required). For example, to instal human reference
genome (hg19):
`source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Hsapiens.UCSC.hg19")`
Corresponding genome packages are required before uploading the files
for plotting. Full list of supported genomes is avilable here:
http://www.bioconductor.org/packages/release/BiocViews.html\#\_\_\_BSgenome
Alternative installation
------------------------
SeqPlots can be directly cloned into Shiny Server application folder
from git repository by using
`git clone https://github.com/Przemol/seqplots.git`. The data location
can be set up with following R code:
`root <- /data/location dir.create(root) setwd(root) require(RSQLite) sqlite <- dbDriver("SQLite") con <- dbConnect(sqlite, dbname = "files.sqlite") dbGetQuery(con, "CREATE TABLE files (id INTEGER PRIMARY KEY ASC, name TEXT UNIQUE, ctime TEXT, type TEXT, format TEXT, genome TEXT, user TEXT, comment TEXT)") if (!dbListTables(con) == "files") warning("Database not created!") dbDisconnect(con) if (!all(sapply(c("removedFiles", "files", "publicFiles", "tmp"), dir.create))) warning("Folders not created!") message("\nData loaction: ", root)`
The following dependencies must be installed in R:
package version
1 shiny 0.10.0
2 fields 7.1
3 parallel 3.1.0
4 multicore 0.2
5 BSgenome 1.32.0
6 GenomicRanges 1.16.3
7 plotrix 3.5-7
8 rtracklayer 1.24.2
9 RJSONIO 1.2-0.2
10 RSQLite 0.11.4
11 kohonen 2.0.14
12 Cairo 1.5-5
13 digest 0.6.4
14 methods 3.1.0
15 tools 3.1.0
16 utils 3.1.0
17 httpuv 1.3.0
18 caTools 1.17
19 xtable 1.7-3
20 htmltools 0.2.4
21 bitops 1.0-6
22 Rcpp 0.11.2
23 spam 0.41-0
24 maps 2.3-7
25 grid 3.1.0
26 grDevices 3.1.0
27 BiocGenerics 0.10.0
28 IRanges 1.22.9
29 Biostrings 2.32.0
30 XVector 0.4.0
31 Rsamtools 1.16.1
32 graphics 3.1.0
33 stats 3.1.0
34 zlibbioc 1.10.0
35 GenomeInfoDb 1.0.2
36 stats4 3.1.0
37 XML 3.98-1.1
38 RCurl 1.95-4.1
39 GenomicAlignments 1.0.1
40 BiocParallel 0.6.1
41 foreach 1.4.2
42 BatchJobs 1.2
43 BBmisc 1.7
44 DBI 0.2-7
45 sendmailR 1.1-2
46 brew 1.0-6
47 plyr 1.8.1
48 stringr 0.6.2
49 fail 1.2
50 checkmate 1.0
51 codetools 0.2-8
52 iterators 1.0.7
53 base64enc 0.1-1
54 class 7.3-10
55 MASS 7.3-33
Adding and managing files
=========================
Supported file formats
----------------------
Tracks:
- BigWig (.bw) - http://genome.ucsc.edu/FAQ/FAQformat.html\#format6.1
- Wiggle (.wig) - http://genome.ucsc.edu/goldenPath/help/wiggle.html
- BedGraph (.bdg) -
http://genome.ucsc.edu/goldenPath/help/bedgraph.html
Features:
- BED - http://genome.ucsc.edu/FAQ/FAQformat.html\#format1
- GFF - http://genome.ucsc.edu/FAQ/FAQformat.html\#format3
- GTF (with .gff extension) -
http://genome.ucsc.edu/FAQ/FAQformat.html\#format4
Files must be formatted according to UCSC guidelines. All widely used
chromosome names conventions are accepted, e.g. for human files either
'chr1' or '1' can be used, however these conventions should not be mixed
within single files.
Adding files
------------
Press the `Add files` button to bring up the **file upload panel**.
> ![File upload panel](img/05_01.png)
You can drag and drop files here or press the `Add files...` button to
open a file selection menu. Before starting the upload the following
mandatory information must be provided about each file:
- User ID
- Reference genome - drop-down menu containing reference genome
package currently installed in R
Comments are optional.
The contents of the text field can be copied to all files by clicking
the icon at the left of the field. The default values can be set using
`Set defaults...` button. Default values are stored using the browser
cookies, and the settings will be remembered across different sessions
as long as the same web browser is used. File extensions that are not
supported will raise an error.
> ![File upload panel with 4 files selected](img/05_02.png)
Individual files can be uploaded by pressing 'start' next to the file
name or all files can be uploaded at once by pressing the `Start upload`
button at the top of **file upload panel**.
During the upload process a progress bar is displayed. After upload
SeqPlots gives a message that upload was successful or or gives an error
message. Common errors are misformatted file formats or chromosome names
do not matched the reference genome. For more information please refer
to **Errors explanations** chapter.
> ![A feedback on successfully upload files](img/05_03.png)
To dismiss the upload window, click on `X` or outside the window.
Downloading and removing files
------------------------------
Clicking the `New plot set` button brings up the **file collection
window**. The primary function of this window is to choose signal tracks
and feature files to use for calculating the plots. However, it also
provides basic file management capabilities. Information on files can be
reviewed and files can be downloaded or deleted. Fields can be searched,
filtered and sorted by any column. The red `x` button on the right site
of file table removes a single file from the collection, while
`Remove selected files` button will erase all selected files.
> ![The file collection window](img/05_04.png)
Running the plot-set jobs
=========================
Pressing the `New plot set` button brings up the **file collection
window** from which you can choose signal tracks and feature files to
calculate average plots and heat maps. The **file collection
window** has three tabs:
- `Tracks` - signal files, i.e., Wiggle, BigWiggle and BedGraph files.
- `Features` - genomic feature files, i.e., BED, GFF and GTF files
- `Sequence features` - input any motif of interest that you want to
plot.
> ![The file collection modal](img/06/06_01.png)
Selecting files
---------------
The `Tracks` and `Features` tabs displays information about the files
and allows you to filter and sort by any column. The "Search:" dialog
allows you to find any keyword in any field, while dropdowns below the
file grid allow for more advanced filtering on specific columns.
Select files by clicking on the file name or any other part of the row
beside `Show comment` and `Download` or `Remove` buttons. Chosen files
are highlighted in light blue. Clicking the file name again will cancel
the selection. At least one signal track or motif and one feature file
must be selected before starting the calculation.
Setting up plot options
-----------------------
Options controlling the plot settings is found below the file selection
window:
1. **`Bin track @ [bp]:`** - this numeric input determines the
resolution of data acquisition; the default value 10 means that 10bp
intervals within the plotting range will be summarized by
calculating the mean. Higher values increases the speed of
calculation and produces smoother plots, but decreases resolution.
2. **`Choose the plot type`** - there are three options:
- *`Point Features`* - anchor plot on the start of a feature. By
default, plot will be directional if strand information is
present (i.e, use start position and plot on positive strand for
+ strand features and use end position and plot on negative
strand for minus strand features). If strand information is not
present in the feature file (or if the "ignore strand" option is
chosen), plot will use start position of feature and be plotted
on the positive strand. User chooses
length of upstream and downstream sequence to plot.
- *`Midpoint Features`* - similar to point feature, but plot is
centered on the midpoint of the feature.
- *`Anchored Features`* - features are anchored at start and stop
positions and given pseudo-length chosen by the user.
Additionally, the user chooses the length of sequence upstream
of the start and downstream of the end to plot.
3. **`Ignore strand`** - the directionality (strand) will be ignored
all features plotted on the positive strand.
4. **`Ignore zeros`** - signal values of 0 in the track will be be
excluded from calculations
5. **`Calculate heatmap`** - selecting this generates and saves a heat
map matrix. Select if you wish to generate heatmap; uncheck if you
only wish to generate average plots, as this will speed
calculations.\
6. **`Plotting distances in [bp]`** - the distances in to be plotted:
- *`Upstream`* - the plotting distance in base pairs upstream to
the feature
- *`Anchored`* - the pseudo-length, to which the features will be
extended or shrunk using linear approximation (only for anchored
plots)
- *`Downstream`* - the plotting distance in base pairs downstream
to the feature
Plotting sequence motif density
-------------------------------
The `Sequence features` tab allows you to calculate and plot the density
of any user-defined motif around the chosen genomic feature using the
reference sequence package. Motif plots can be mixed with track files'
signal plots. The following options can be set:
1. **`DNA motif`** - the DNA motif
2. **`Sliding window size in base pairs [bp]`** - the size of the
sliding window for motif calculation. The value (number of matching
motifs within the window) is reported in the middle of the window,
e.g. if window is set to 200bp, DNA motif is "GC" and there are 8
CpGs in first 200 bp of the chromosome the value 8 will be reported
at 100th bp.
3. **`Display name`** - The name of the motif that will be shown in key
and heatmap labels. Leave blank to use `DNA motif` value.
4. **`Plot heatmap or error estimates`** - this checkbox determines if
heatmap matrix and error estimates should be calculated. If
unchecked much faster algorithm will be used for motif density
calculation, but only the average plot without the error estimates
will be available.
5. **`Match reverse complement as well`** - select if reverse
complement motif should be reported as well. For example the TATA
motif will report both TATA and ATAT with this option selected.
> ![Sequence motifs selection tab](img/06/06_02.png)
Clicking `Add` button adds the motif to plot set, while `Reset All`
clears the motif selection. On the right side of the motif setting panel
gives a list summary of included motifs.
Starting the plot set calculation
---------------------------------
The option are executed by pressing `Run calculation` button. This
dismisses the **file collection window** and brings up the calculation
dialog, which shows the progress. On Linux and Mac OS X (systems
supporting fork based parallelization) the calculation can be stopped
using the `Cancel` button - this will bring back all settings in **file
collection window**.
> ![The calculation progress dialog](img/06/06_03.png)
After the successful execution the **plot array** will appear. In case
of error an informative error pop-up will explain the problem. Please
refer to the error section for further information.
> ![The plot array](img/06/06_04.png)
Plotting
========
> This section focuses on average (line) plots and options common
> between these and heatmaps. For heatmap options please refer to
> heatmap documentation.
Previewing plot
---------------
After calculating or loading a plot set, a **plot array** of checkboxes
is displayed to select the desired pairs of features and tracks/motifs.
Clicking on the column name (tracks/motifs) or row name (features)
selects/deselects the whole column or row. Clicking on top-left most
cell of **plot array** toggles the selection of whole array.
> ![Plot preview plus `Line plot`, `Heatmap` and `refresh`
> buttons](img/07_01.png)
If at least one pair on **plot array** is selected pressing the
`Line plot` button produces an average plot preview and the `Heatmap`
button produces a heatmap preview. Alternatively, pressing the [RETURN]
key will also produce the new selection and options. These operations
are done automatically in `reactive mode` (see **Advanced options**). Plots can be
downloaded as PDF files using the Line plot and Heatmap buttons next to
Download (at the top of the panel).
> ![The tab selection area - icons represnts seven
> panels](img/07_02.png)
Below the plotting buttons are options for labeling plots and setting
axes. On application start the first panel responsible for bringing file
upload, management and plot set calculation modals is active. The
further three panels hold common plot settings.
Titles and axis panel
---------------------
This panel groups settings influencing the plot main title, axis labels,
various font sizes plus vertical and horizontal plot limits.
- `Title` - The main title of the plot, shown in top-center part of
the figure; default empty
- `X-axis label` - Label shown below horizontal axis; default empty
- `Y-axis label` - Label shown below vertical axis; default empty
- `Title font size` - Font size of the title in points (point = \~1/72
an inch for standard A4 output); default 20 points
- `Labels font size` - Font size of axis labels in points; default 16
points
- `Axis font size` - Controls axis ticks font size, that is size of
the numbers indicating position in base pairs on X-axis and means
signal value on X-axis; default 14 points
- `Set X-axis limits` - Set hard plotting limits for X-axis; default
values are whole range chosen during plot set calculation
- `Set Y-axis limits` - Set hard plotting limits for Y-axis; default
values are a range between lowest and highest mean signal extended
by error estimate
> ![The view on titles and axis panel](img/07_03.png)
Guide lines and data scaling
----------------------------
Controls in this panel controls the display of guide lines and error
estimates, and allows to log scale the signal prior to plotting.
- `Transform signal` - if set to *`Log2 transform`* performs log2
transformation of the signal prior to plotting; default setting is
*`Do not transform`*
- `Show vertical guide line` - show the vertical line at point 0 -
beginning of the feature or midpoint and end of the pseudo-length
scaled features (only for anchored plots); turn on by default
- `Show horizontal guide line` - show the horizontal line at user
determined height; turn off by default
- `Show error estimates` - show error standard error and 95%
confidence interval as fields, if turned off only the line
representing the mean signal is shown; turn on by default
> ![The view on guide lines and data scaling](img/07_04.png)
Keys, labels and colors panel
-----------------------------
This panel groups two types of controls. `Colors`, `Label` and
`Priority/Order` are a checkboxes revealing further controls on **plot
set grid**, specific for a feature-track pair or sub-heatmap.
`Show plot key`, `Show error estimate key` and `Legend font size` re
global controls specific for average plots. Inputs on **plot set grid**
do not have specific labels, but the tooltip explaining their meaning is
shown on mouse cursor hover.
- `Colors` - checkboxes revealing a color picker on **plot set grid**.
This input allows to control the colors of specific feature-track
pair average plots or sub-heatmaps. In browser supporting the color
picker 'e.g Chrome' the system dialog will show up. In other
browsers (e.g. Firefox) the javaScript color picker will be
initialized.
- `Label` - checkboxes revealing a label text input **plot set grid**.
This controls the names shown on the **key** with average plots or
the heatmap top labels.
- `Priority/Order` - checkboxes revealing numeric input on **plot set
grid**. These number determine the order of average plots and
hetamaps. Feature-track pair with the highest priority will be
listed on the top of **key** for average plots and left-most for
heatmaps.
- `Show plot key` - shows the key giving the color to feature-track
pair label mapping. If turned on the additional drop-down allows to
choose the position on the plot, top-right by default
- `Show error estimate key` - shows the key gexplaining the meaning of
error fields. If turnedon the additional drop-down allows to choose
the position on the plot, top-left by default
- `Legend font size` - set the size of font used to plot the keys; 12
default
> ![The view on keys, labels and colors panel (left). Color picker,
> label text input and Priority/Order checkboxes reviled on plot set
> grid (right).](img/07_05_06.png)
Plotting and setting up heatmaps
================================
Heatmaps are often more informative than average plots. If there is
variability in signal along individual instances of a given genomic
feature (e.g., because there are different biological classes), an
average plot might not represent the behavior of any individual feature
and could even give a misleading picture. SeqPlots plots track-feature
pairs as sub-heatmaps horizontally aligned on single figure. All
sub-heatmaps must have the same number of data rows, hence in single
plot mode simultaneous plotting is possible only on single features or
feature files containing exact same number of rows. The heatmaps can be
sorted and clustered by k-means, hierarchical clustering or super self
organising maps (SupreSOM).
> ![An example of heatmap plot](img/08_01.png)
Heatmap setup tab
-----------------
This tab has heatmap specific options for data processing and display.
> ![The view on Heatmap setup tab (left). Color picker, Label text
> input, Priority/Order checkboxes, Choose individual heatmaps for
> sorting/clustering control and Set individual color key limits numric
> inputs reviled on plot set grid (right).](img/08_02.png)
- **`Sort heatmap rows by mean signal`** - sorts the heatmap rows
based on the mean value of each row across included sub-heatmps. Can
be set to increasing or decreasing order. Turned off by default.
- **`Clustering algorithm`** - choose clustering algorithm (k-means,
hierarchical or SupreSOM). If clustering is not desired, choose
*`do not cluster`*, which uses the feature file in the uploaded
order . K-means by default.
- **`Make cluster calculation repeatable`** - enforces, that
clustering with non-deterministic algorithms, like k-means or
SupreSOM will generate the same results as most recently plotted
heatmap. This is achieved by re-using R random number generator
seed.
- **`Plot cluster only selected`** - this option is available only if
`Make cluster calculation repeatable` is turned on. Allows to select
one of the clusters and zoom it to whole plot height. Plot all
clusters by default.
- **`Choose individual heatmaps for sorting/clustering`** - this
checkbox brings up a new control panel on the **plot set grid** to
determine if a given sub-heatmap should be included in plotting
and/or clustering. The excluded sub-plots will be plotted in the
order of the other sub-heatmaps, but their values will not influence
the clustering/sorting. By default all sub-heatmaps are included.
Following example shows hierarchical clustering on both heatmaps
included (left) and second heatmap excluded (right):
> ![`Choose individual heatmaps for sorting/clustering` usage
> example: hierarchical clustering on both heatmaps included (left)
> and second heatmap excluded (right)](img/08_03.png)
- **`Heatmaps have individual color keys`** - this option determines
if each sub-heatmap should have a separate color key (plotted below
the heatmap) or a single, common key should be calculated for all
sub-plots (plotted rightmost). By default all sub-heatmap have their
own color keys. The example below show the difference between
separate (left) and common (right) color keys:
> ![`Heatmaps have individual color keys` usage example: separate
> (left) and common (right) color keys](img/08_04.png)
- **`Set default color key limits`** - this option determines the
limits in mapping the numerical values to the colors. The range of
colors generated is dependent on these options. Values lower or
higher than the given limits will be plotted in the limit value
color. If this checkbox is not selected, limits are auto-generated
using **`Color key scaling`** parameter. If this option it turned
off two numerical fields, **`min`** and **`max`**, are shown to
manually set the limits.
- **`Color key scaling`** - this slider influences how color key
limits are generated. For example, 0.01 (default value)
calculates limits using data ranging from 1-99 percentile of
available data points. 0.1 uses data ranging from 10-90
percentile. The general formula for limit is: [quantile(data,
`Color key scaling`); quantile(data, 1-`Color key scaling`)]
- **`min`** and **`max`** numeric inputs - enter values to
manually specify color key limits as numeric values.
- **`Set individual color key limits`** - this option is similar to
manual set up of color key limits, but this allows one to specify
different values for individual sub-heatmaps. When this checkbox is
selected **`min`** and **`max`** numeric input menu is shown on the
**plot set grid**
- **`Set default colorspace`** - When this option is selected three
color pickers are shown to set up custom color mappings for
heatmaps. The following example below shows standard jet colors
(left), default blue color mapping after selecting the checkbox
(middle) and custom color selection (right):
> ![`Set default colorspace` usage example: standard jet colors (left),
> default blue color mapping after selecting the checkbox (middle) and
> custom color selection (right)](img/08_05.png)
Other options controlling heatmap appearance
--------------------------------------------
The heatmap output shares many display options from other tabs. Here we
provide a list of these inputs.
- **Titles and axis panel**
- `X-axis label` - Label shown below horizontal axis, drawn
separately for each sub-heatmap; default empty
- `Y-axis label` - Label shown next to vertical axis, drawn
separately for each sub-heatmap; default empty
- `Labels font size` - Font size for axis labels and main labels
of sub-heatmaps; default 16 points
- `Axis font size` - Controls axis ticks font size; default 14
points
- `Set X-axis limits` - Set hard plotting limits for X-axis;
default values are whole range chosen during plot set
calculation
- **Guide lines and data scaling panel**
- `Transform signal` - if set to *`Log2 transform`* performs log2
transformation of the signal prior to plotting; default setting
is *`Do not transform`*
- `Show vertical guide line` - show the vertical line at point 0 -
beginning of the feature or midpoint and end of the
pseudo-length scaled features (only for anchored plots); turn on
by default
- **Keys, labels and colors panel**
- `Colors` - for hetmaps this input allows to control the color
mapping of specific sub-heatmaps. The map starts with white (for
low color key limit) and finishes with selected color (for high
color key limit).
- `Label` - allows to set up custom sub-heatmap top labels
- `Priority/Order` - Use this to place heatmaps in your desired
order. The feature-track pairs with the highest priority will be
plotted as left-most sub-heatmaps.
- `Legend font size` - control the font size of common color key,
inactive if heatmaps have individual color keys; 12 default
Downloading output files and batch operations
=============================================
Plots can be downladed as PDFs by clicking `Line plot` or `Heatmap`
buttons in the "Download:" section of the **tool panel** (above the plot
preview).
> ![Download:" section of tool panel with `Line plot` and `Heatmap`
> buttons](img/09_01.png)
The small buttons next to `Line plot` and `Heatmap` produce additional
output files:
- the `i` button next to `Line plot` downloads the PDF containing
average plot keys
- `cluster diagram` button next to `Heatmap` downloads a cluster
report giving cluster assignments and sorting order for each feature
as a comma separated value (CSV) spreadsheet.
The cluster report contains following columns:
- `chromosome` - the name of chromosome, contig or scaffold
- `start` - start of the feature (1 based chromosomal coordinate)
- `end` - end of the feature (1 based chromosomal coordinate)\
- `width` - width of the feature in base pairs
- `strand` - strand of the feature
- `metadata_...` - annotation columns present in the original GFF/BED
e.g. gene name, score, group
- `originalOrder` - number of feature (row) in GFF/BED, can be used to
restore original order after sorting on cluster ID
- `ClusterID` - the numeric ID of the cluster. The topmost cluster on
the heatmap is annotated with 1, and the bottom cluster with k,
where k equals to number of clusters selected, exported only if
clustering is enabled
- `SortingOrder` - the order imposed on heatmap by sorting by mean
row(s) values, exported only if sorting is enabled
- `FinalOrder` - the final order of heatmap's rows, this can be
influenced by sorting and clustering; 1 indicates topmost row
Sample report:
chromosome start end width strand metadata_group originalOrder ClusterID SortingOrder FinalOrder
chrI 9065087 9070286 5200 + g1 1 1 3 3
chrI 5171285 5175522 4238 - g1 2 3 50 43
chrI 9616508 9618109 1602 - g1 3 3 13 43
chrI 3608395 3611844 3450 + g1 4 3 11 12
PDF output size
---------------
The last tab (`Batch operation and setup`) on the **tool panel**
includes batch operations and various other settings including PDF
output size. By default the output PDF will be A4 landscape. This can be
changed using the drop-down list to following settings:
- `user defined` - this option reveals two numeric inputs that allows
to set output PDF width and height. The values must be given in
inches.
- `Legal rotated` - US Legal landscape: 14" by 8.5"
- `A4` - A4 portrait: - 8.27" × 11.69"
- `Letter` - US Letter portrait: 8.5" × 11"
- `Legal` - US Legal portrait: 8.5" × 14"
- `Executive` - a.k.a Monarch paper: 7.25 × 10.5"
> ![The view on top part of batch operation and setup
> panel](img/09_02.png)
Batch operations
----------------
Controls to plot multiple plots at once are located on the
`Batch operation and setup` tab, just below PDF paper options. It is
possible to output the plots to multipage PDF, plot an array of plots on
a single page (for average plots) or mix these options together.
> ![The view on bottom part of batch operation and setup
> panel](img/09_03.png)
The first drop-down controls the type of the plot - either average or
heatmap. The second drop down determines the strategy to traverse the
**plot grid**. The options include:
- `single` - every single feature-track pair will be plotted on
separate plot
- `rows` - the **plot grid** will be traversed by rows, which means
one plot that contains all tracks per feature will be prepared
- `columns` - the **plot grid** will be traversed by columns, which
means one plot that contains all features per tracks will be
prepared
The `multi plot grid` option controls how many plots will be placed on
each page of the PDF output, e.g. 1x1 means one plot per one page, while
3x4 means 3 columns and 4 rows of plots. If number of plots exceeds the
number of slots on page the new page will be added to the PDF.
`Filter names` will apply a filter to plot titles, which are based on on
uploaded file names. For example, if you uploaded 100 files starting
with a prefix of "my\_experiment\_", you can remove this fragment from
each plot title and/or heatmap caption by putting this string in
`Filter names`.
Finally, pressing `Get PDF` produces the final output file. Please see
example below:
> ![Batch plot usage example - multiple average plots aranged in 6x2
> plot grid](img/09_04.png)
Saving plotsets and loading previous plot sets
==============================================
If desired, SeqPlots will save plot sets as binary R files, allowing you
to quickly load the pre-calculated set for replotting. Saved plot sets
can also be shared with other SeqPlots users.
Load or save plotset
--------------------
Controls available on the "Load or save plotset" panel:
- **`Load saved plot set`** - drop-down list to select a plotset. Once
the Rdata binary file is selected the **plot grid** will be
displayed. Selecting the file reveals two additional buttons:
- **`Remove dataset`** - this button deletes the selected saved
plot set from user data.
- **`Download plotset`** - this button saves a copy of the plotset
in selected location.
- **`Save current plot set`** - Enter desired name and press the
`Save` button (appears after input of name). It is also possible to
save a copy of loaded plot sets. The plot set binary files can be
renamed simply by loading them, saving a copy and deleting original
source file.
All saved dataset can be found in `data location`/publicFiles. Any
SeqPlots Rdata binaries put in the folder will become available for
loading in **`Load saved plot set`** control.
> ![The view on the "Load or save plotset" panel](img/10_00.png)
Plot set files structure
------------------------
The plot sets files can be also directly loaded in R. This allows
further processing and customization of the plots. Data structure is a
nested list, which elements be accessed by `[[` R operator. The nesting
goes as follow:
- **`feature`** - R list
- **`track`** - R list
- `means` - numeric vector giving mean signal value for each
(binned) genomic position
- `stderror` - numeric vector giving standard error for each
(binned) genomic position
- `conint` - numeric vector giving 95% confidence interval for
each (binned) genomic position
- `all_ind` - numeric vector giving the genomic position in
base pairs
- `e` - character string giveing numeric vector giving the
indicates of anchored distance, NULL for point features
plots
- `desc` - auto generated title of the plot
- `heatmap` - numeric matrix, (binned) signal values for each
genomic position (columns) and each feature (rows)
The example structure:
```
List of 2
$ HTZ1_Differential_genes_TOP100_v2.gff:List of 2
..$ HTZ1_JA00001_IL1andIL2_F_N2_L3_NORM_linear_1bp_IL010andIL009_averaged.bw :List of 7
.. ..$ means : num [1:501] 2.52 2.52 2.52 2.53 2.54 ...
.. ..$ stderror: num [1:501] 0.114 0.112 0.111 0.11 0.109 ...
.. ..$ conint : num [1:501] 0.226 0.223 0.221 0.218 0.217 ...
.. ..$ all_ind : num [1:501] -1000 -995 -990 -985 -980 -975 -970 -965 -960 -955 ...
.. ..$ e : NULL
.. ..$ desc : chr "HTZ1_JA00001_IL1andIL2...\n@HTZ1_Differential_genes_TOP100_v2"
.. ..$ heatmap : num [1:100, 1:501] 2.36 5.25 2.2 3.48 4.32 ...
..$ HTZ1_JA00001_IL3andIIL5_F_lin35_L3_NORM_linear_1bp_IL008andIL011_averaged.bw:List of 7
.. ..$ means : num [1:501] 2.36 2.35 2.35 2.36 2.38 ...
.. ..$ stderror: num [1:501] 0.126 0.125 0.125 0.126 0.125 ...
.. ..$ conint : num [1:501] 0.249 0.249 0.247 0.251 0.249 ...
.. ..$ all_ind : num [1:501] -1000 -995 -990 -985 -980 -975 -970 -965 -960 -955 ...
.. ..$ e : NULL
.. ..$ desc : chr "HTZ1_JA00001_IL3andIIL5...\n@HTZ1_Differential_genes_TOP100_v2"
.. ..$ heatmap : num [1:100, 1:501] 2.61 3.17 1.42 2.46 4.26 ...
$ HTZ1_Differential_genes_BOTTOM100.gff:List of 2
..$ HTZ1_JA00001_IL1andIL2_F_N2_L3_NORM_linear_1bp_IL010andIL009_averaged.bw :List of 7
.. ..$ means : num [1:501] 1.57 1.57 1.58 1.6 1.62 ...
.. ..$ stderror: num [1:501] 0.0996 0.0985 0.1003 0.1022 0.1018 ...
.. ..$ conint : num [1:501] 0.198 0.195 0.199 0.203 0.202 ...
.. ..$ all_ind : num [1:501] -1000 -995 -990 -985 -980 -975 -970 -965 -960 -955 ...
.. ..$ e : NULL
.. ..$ desc : chr "HTZ1_JA00001_IL1andIL2...n@HTZ1_Differential_genes_BOTTOM100"
.. ..$ heatmap : num [1:100, 1:501] 1.64 1.37 1.61 1.77 1.86 ...
..$ HTZ1_JA00001_IL3andIIL5_F_lin35_L3_NORM_linear_1bp_IL008andIL011_averaged.bw:List of 7
.. ..$ means : num [1:501] 1.94 1.94 1.95 1.96 1.97 ...
.. ..$ stderror: num [1:501] 0.123 0.123 0.124 0.126 0.128 ...
.. ..$ conint : num [1:501] 0.244 0.245 0.246 0.251 0.253 ...
.. ..$ all_ind : num [1:501] -1000 -995 -990 -985 -980 -975 -970 -965 -960 -955 ...
.. ..$ e : NULL
.. ..$ desc : chr "HTZ1_JA00001_IL3andIIL5...\n@HTZ1_Differential_genes_BOTTOM100"
.. ..$ heatmap : num [1:100, 1:501] 1.61 1.37 1.29 3.04 3.77 ...
```
Advanced options
================
Some additional SeqPlots options are located at very bottom of the `Batch operation and setup` tab:
> ![The view on 'Advanced options' section of the batch operation and setup panel](img/10_01.png)
* `Keep 1:1 aspect ratio in batch mode` - This option guarantee that the ratio between X- and Y-axis height will be 1, hence the produced plots will be square in batch mode. This prevents stretching the plots while fitting single rows or columns to one page. Turned on by default.
* `Always keep 1:1 aspect ratio` - This checkbox extends the 1:1 aspect ratio option to single plots. Turned off by default.
* `Reactive plotting` - When selected, all plotting operations are executed upon selection and will be visible in preview. `Reactive plotting` might be useful for exploratory data analysis using plots, but it is not recommended for heatmap plots because speed is decreased. Select/delelect from keyboard by pressing [ctrl/cmd+R]. Turned off by default.
* `Use multithreading for calculations` - This option is available only on desktop instances of SeqPlots under Mac OS X and Linux. While turned off R will not fork the child processes for plotting and plot set calculations. It is useful for debugging, since in single process mode all warning/errors will be directly printed to R console. Also might increase the performance for plotting small average plots. Turned off by default.
* `Use ggplot2 graphics package for heatmaps` - uses GGplot2 (http://ggplot2.org/) graphics system to draw the heatmaps. This feature is experimental.
Error messages
==============
```
Problem with line N: "line_text" [internal_error]
```
> The import of feature file (GFF or BED) was not successful due to mis-formatted file.
-----------------
```
Chromosome names provided in the file does not match ones defined in reference genome.
INPUT: [chr3R, chr2L, chr2R, chr3L]
GENOME: [chrI, chrII, chrIII, chrIV, chrV, ...]
```
> There are unexpected chromosome names in input file. Following genomes: *Arabidopsis thaliana, Caenorhabditis elegans, Cyanidioschyzon_merolae, Drosophila melanogaster, Homo sapiens, Oryza sativa, Populus trichocarpa, Saccharomyces cerevisiae and Zea mays* support chromosome names remapping between different naming conventions, including: AGPv2, ASM9120v1, Ensembl, JGI2_0, MSU6, NCBI, TAIR10 and UCSC. If you see above error in one of these genomes there are still unexpected names after the correction.
The problematic chromosome names are given in the error message. Remove GFF/BED lines corresponding to them or upgrade the genome to one containing proper naming. Alternatively set genome to NA.
-----------------
```
File already exists, change the name or remove old one.
```
> File named like this already exists in the database, it is impossible to have two files sharing same filename.
-----------------
```
ERROR: solving row 300: negative widths are not allowed
```
> The the row 300 have end coordinate smaller than beginning, hence the width in negative. To fix it the start and stop indicates should be swapped. This error often happens when negative strand (-) ranges are misformatted.
-----------------
Version history
===============
CHANGES IN VERSION 1.2.0
------------------------
PACKAGE:
- plot a dendrogram as first panel on heatmap plot clustered with
hierarchical clustering
- heatmap can be plotted as vector graphics (default for R scripting)
or raster graphics (default for web GUI)
- heatmaps can be sorted in increasing or decreasing order
- y-axis is annotated with cluster IDs and number of data rows
(heatmap)
- x-axis is annotated with base pairs, e.g. 10bp, 1kb, 1.2Mb, etc.
- heatmaps can be plotted using GGplot2 package instead of R base
graphics system
- speed-up in motif plots thanks to faster, vectored implementation of
motif density data acquisition
- code simplification - seqplots in Shiny GUI mode use all functions
from package core
GUI:
- feature-track pairs selection grid have UI elements to multi-select
and batch change labels/colors/etc.
- option to make a clustering repeatable (works by reusing a
.Random.seed)
- option to plot selected cluster only as heatmap
- SeqPlots GUI updated to work with Bootstrap v3.3.1
BUGFIX:
- lines separating the clusters are drawn in correct places on
grDevices::quartz devices
- proper positioning of 3' ends of anchored region in motif plot
- fixed error with anchored plots and genomic feature width equals 1bp
- y-axis does respect cex.axis parameter
- GUI fixed to work with shiny 0.11.0 and above
CHANGES IN VERSION 1.0.0
------------------------
PACKAGE:
- plotHeatmap function returns cluster report as GRanges structure
- redundant parameters removed from plotting functions
- plotHeatmap function have "embed" parameter for plotHeatmap - allows
to plot 1st heatmap without using grid system, intended to use with
complex plots
BUGFIX:
- motif plot orientation properly dependents on strand
- GUI - reordering the heatmap respects previously set include/exclude
parameters
CHANGES IN VERSION 0.99.1
-------------------------
PACKAGE:
- heatmap plotting function returns cluster report ad data.table
- getPlotSetArray function have "verbose" parameter that controls
messages and warnings output
- references added to documentation
BUGFIX:
- plotHeatmap and plotAverage generic methods for SeqPlots-classes
respect the parameters
- package passes tests and check on 32bit Windows (plotting only,
because no rtrackalyer::BigWigFile support for Win32)
CHANGES IN VERSION 0.99
-----------------------
GENERAL:
- Anchored plots and heatmaps uses [downstream]--0--0--[upstream]
X-axis coordinate system instead
[downstream]--0--[anchored]-[upstream+anchored]
PACKAGE:
- package really on reference class system including MotifSetup,
PlotSetArray, PlotSetList and PlotSetPair
- generic subset and data manipulation methods for SeqPlots-classes
including '[', "[[" and "unlist", which allows to switch between
classes
- automatic tests for class system, calculations and plotting
functions
- documentation for all functions and classes
- PDF vignette engine replaced by HTML one
- QuickStart vignette added
GUI:
- automated GUI tests using Rselenium package
BUGFIX:
- issue \#1: some server instances loads empty .Rdata file on startup
CHANGES IN VERSION 0.9.3
------------------------
- The web GUI and R package projects merged into singe project
distributed as Bioconductor compatible R package
- The command line interface have the same capabilities as GUI version
- Web GUI vignette added
CHANGES IN VERSION 0.9.2
------------------------
GENERAL:
- use Cairo package for plotting, X11 installation no longer required
- colors in plot grid are initiated automatically (same color palette
as for auto-generated average plots), white color is allowed
- more informative error messages during file upload
- documentation is integrated with SeqPlots GUI help
- Web GUI debug console added
- Exit button, that closes web interface and background R process
BUGFIX:
- fixed errors reporting in singe core/Windows mode
- the custom color gradient controls for hetmap (three color pickers)
work correctly now
- heatmap main title no longer overlaps with sub-plot labels
CHANGES IN VERSION 0.9.1
------------------------
GENERAL:
- inputs and features sorted alphabetically
- DataTables v1.10.0 with pagination, selection number indicator and
infinite row selections
- buttons for heatmap and lineplots, PDF default sizes,
- changes in GUI layout
- default PDF output paper size set to A4 horizontal,
- Font sizes are in points
- preview is compatible with A4 PDF output (at 100 DPI)
- color key for heatmap are always generated using image.plot function
that provides better labeling
- batch plots do not override individual labels if set
- option to keep 1:1 aspect ratio (default for batch plots)
- miscellaneous options renamed for clarity
CHANGES IN VERSION 0.9.0
------------------------
FEATURES:
- Multi-plot grid option in batch mode - many line plots on single
page
GENERAL:
- R 3.1 and BioC 2.14 compatibility
- faster BigWig signal retrieval, no need for modified rtracklayer C
code in the package
- warning message if JS File API is not supported (old browsers)
- improved the performance of heatmap plotting by using list of
matrices instead concatenated matrix
BUGFIX:
- application start properly without any BSGenome genomic packages
installed
- cluster report - the final order agrees with cluster indicates
CHANGES IN VERSION 0.8.2
------------------------
FEATURES:
- Hierarchical and super self-organizing network clustering added for
heatmaps
- Anchored motif plots
- The row order of the heatmap is exported along with cluster report
GENERAL:
- JS color picker added for browsers, that do not support select input
type="color" i.e. Firefox (checked with modernizr.js library)
- Single process mode and Microsoft Windows compatibility (running
without fork parallelization)
- Shiny 0.9.1 compatibility
- Saved datasets can be downloaded for local usage
- Clicking row or column name in plot grid toggles the checkboxes
- Minor GUI changes
CHANGES IN VERSION 0.8.1
------------------------
GENERAL:
- GUI redesign: plot matrix incorporates sub-plot/heatmap specific
controls, all heatmap options gathered in single tab
- warning before closing/refreshing a webpage with active session
- cookie based default options: user, genome and deactivate page exit
warning
- heat-map clusters provided as cluster report - a CSV file containing
original features, annotations and cluster information, see more:
https://bitbucket.org/przemol/seqplots/wiki/Heatmaps\#markdown-header-cluster-report
- Wiggle files processing: correct for multiple header definitions and
roman/arabic chromosome names correction
- Optimised keyboard shortcuts: plot - RETUTRN or ctrl/cmd+SPACE,
switch heatmap - ctrl/cmd+H, switch reactive plotting - ctrl/cmd+R
- minor speed improvement
BUGFIX:
- Motif density plots and heatmaps: flip rows on (-) strand
CHANGES IN VERSION 0.8.0
------------------------
GENERAL:
- GUI redesign, option partitioned to more tabs
- preview plot is zoomed on click rather than on mouse hover
- possibility to remove multiple files
- comments visible as popup in file managmed window
- all chromosome naming conventions (most notably chrX/X and variants
of chrM/M/MtDNA/MT etc.) are accepted
(http://www.bioconductor.org/packages/release/data/annotation/html/seqnames.db.html)
- incoming featurefiles (GFF and BED) are not processed, just chacked
for errors
- explicit error handling for incoming flies, the line with problem or
unexpected chromosome(s) are indentified to the user
- motif density tracks can be binned (defoult at 10bp)
- tracks amd motif densities cna be mixed together in plots
SERVER:
- server\_config.R added - a configuration file that allows to set up
server varaiables, e.g. the user data location
MAC OS X APP:
- interface to insrall new genomes from Bioconductor and local
resources (R BSgemome format:
http://www.bioconductor.org/packages/release/bioc/html/BSgenome.html)
- option to set up data location
CHANGES IN VERSION 0.7.0
------------------------
- SeqPlots for Mac OS X relesed - an user frienddly wrapper app
containig R, packages and SeqPlots coede
- heatmap plotting added
- motif denstty plotting added for lineplot and heatmap
- minior interface redesign
- reactive interface can be turn off for plottting, user plots on
demend
- adding files from jQuery File Upload
(http://blueimp.github.io/jQuery-File-Upload/) is handled directly
by R eliminating additional node.js server application and making
proper file handling for desktop version
- computationally expensive operations (calculating plot matrix and
plotting) are handeled by new R process (parallel R library) - many
proces can run simmutainously in same Shiny instance, user can get
fedback from the calcualtion can be cancelled
CHANGES IN VERSION 0.6.0
------------------------
- Shiny (https://github.com/rstudio/shiny) used as R web fraimwork,
support for Rserver/EXT JS version dropped
- support for 145 genomes from UCSC database (via user provideing
valid genome symbol)
- new reactive user interface
- new plot type: midpoint features - it calculates the middle of given
features and centres the summary on it
- the option to ignore the strand (plot always in the same direction)
- the option to remove the zeros (0 value of score in Wiggle track)
from mean and error estimate calculations
- the support for BED feature files (in addition to GFF, Wiggle (all
variants), BigWiggle)
- automatic chromosome name correction for C. elegans genomes (I =\>
chrI, MtDNA =\> chrM, etc.)
- accepts wiggle with overlapping ranges (e.g. microarray experiments
processed using MA2C)
- basic user management for uploaded files
- option to download the features and track files directly from
application
CHANGES IN VERSION 0.5.0
------------------------
- Initial test and alpha releases
Glossary
========
-----------
- "**feature**" - a genomic interval defined by **chromosome** name,
**start** and **end** positions and the **directionality** (strand).
The end must always be a bigger number than start, so the width of
the range is not negative. Start and end means here the numeric
start of the interval and should not be confused with TSS and TTS.
For example, in BED format this information is stored in following
text tab delimited format: `chr7 127471196 127472363 . . +`
-----------
- "**directionality**" - the strand of genomic feature, determining if
the plotting range should be anchored around the star or and, and
the direction in which signal is being processed to create the
average track or heatmap. Unknown directionality is marked by `*`
and treated as `+` for calculations.
-----------
- "**track**" - the file assigning the continuous signal (score) to
genomic locations across the chromosomes. The signal usually comes
from sequencing experiments, like ChIP-seq, RNA-seq, DNase-seq,
MNase-seq, or from computational tools, for example nucleosome
occupancy prediction, CpG density.
For example, in BedGraph format this information is stored in
following text tab delimited format: `chr19 49302300 49302600 -0.75`
-----------
- "**reference genome package**" - the R BSgemome package containing
the full reference sequence for given species. It is also used to
provide universal chromosome names and chromosome lengths taht are
used as plotting boundaries.
-----------
- "**reads coverage**" - The basic way to calculate the signal from
sequencing based assays. The numeric representation shows how much
reads was aligned to given genomic location. This can be a proxy to
protein-DNA binding (ChIP-seq) or the expression (RNA-seq). Can be
calculated using BedTools:
http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html
Also known as `pileups`.
-----------


class JoinClause
Properties
| Builder | $query | The query builder instance. |
| string | $type | The type of join being performed. |
| string | $table | The table the join clause is joining to. |
| array | $clauses | The "on" clauses for the join. |
Methods
| void |
__construct(Builder $query, string $type, string $table)
Create a new join clause instance. |
|
| JoinClause |
on(string $first, string $operator, string $second, string $boolean = 'and', bool $where = false)
Add an "on" clause to the join. |
|
| JoinClause |
orOn(string $first, string $operator, string $second)
Add an "or on" clause to the join. |
|
| JoinClause |
where(string $first, string $operator, string $second, string $boolean = 'and')
Add an "on where" clause to the join. |
|
| JoinClause |
orWhere($first, $operator, $second)
Add an "or on where" clause to the join. |
Details
at line 41
public void
__construct(Builder $query, string $type, string $table)
Create a new join clause instance.
at line 58
public JoinClause
on(string $first, string $operator, string $second, string $boolean = 'and', bool $where = false)
Add an "on" clause to the join.
at line 75
public JoinClause
orOn(string $first, string $operator, string $second)
Add an "or on" clause to the join.
at line 89
public JoinClause
where(string $first, string $operator, string $second, string $boolean = 'and')
Add an "on where" clause to the join.
at line 103
public JoinClause
orWhere($first, $operator, $second)
Add an "or on where" clause to the join.


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