-
Notifications
You must be signed in to change notification settings - Fork 25
Versions
Przemol edited this page Sep 15, 2015
·
15 revisions
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
- New package version for Bioconductor 3.1 release
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
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
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)
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
- 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
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
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
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
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
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
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
- 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
- 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
- Initial test and alpha releases