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