inst/seqplots/www/help/Versions.md

In Przemol/seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

Versions history

CHANGES IN VERSION 1.4.1

PACKAGE:

• RJSONIO replaced with jsonlite package for encoding/decoding JSON
• Sub-heatmaps accepts multilevel color palettes in plotHeatmap function
• Better dendrogram positioning for heatmaps with hclust and single sub-heatmap

GUI:

• "Load saved plot set" select input replaced with searchable selectize input
• Tracks and feature names are shown without extensions
• Plot Preview GUI elements are shown directly after calculation finishes or save dataset si loaded, even if no pair is selected.
• Download buttons moved to bottom of side panel
• Color palettes from RColorBrewer package can be selected in GUI
• Web interface tab for managing the reference genomes

BUGFIX:

• Plot Preview shows up when needed with shiny 0.12.0 (issue #6)
• Heatmap top labels and color key font sizing works properly
• Clustering report download works when source feature file were deleted

CHANGES IN VERSION 1.3.0

• New package version for Bioconductor 3.1 release

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

Przemol/seqplots documentation built on May 14, 2022, 6:47 a.m.