When quantifying or loading PSI values, psichomics discards splicing events whose junctions:
(1) are not present in junction quantification data or
(2) have low numbers of reads across all samples.
The number of discarded events is now displayed during PSI quantification.
When normalizing gene expression, support converting gene identifiers to gene symbol names for any species with OrgDb data
Allow to use plotSplicingEvent() directly with a PSI table to plot diagrams of the alternative splicing events within
Distribution plots (plotDistribution()):
Plot sample distributions in density, violin or box plots (argument type in command-line interface)
Hide rug plot when showing 500 or more values (by default) to avoid performance issues
Add jitter to rug plot (helps to discern numerous points)
Display interquantile range (IQR) per group in the tooltip
Add subtitles (argument subtitle in command-line interface)
Allow to invert axes (argument invertAxes in command-line interface)
Bug fixes and minor changes
loadLocalFiles(): print elapsed time after loading local files
filterGroups() was modified to return a character vector whose names are original names (instead of groups) and include an attribute Groups with the respective group of each value (together with their colour, if available):
Distribution plots in the graphical interface now show sample name in the tooltip for each sample
Importing VAST-TOOLS annotation:
Fix parsing of VAST-TOOLS intron retention events as skipped exon for certain annotations (including Hs2)
Support diagrams for intron retention events with full exon coordinates
Graphical user interface improvements:
Avoid "Matching subjects to their samples/Matching process concluded" loop
Timeout GTEx data retrieval after 3 seconds without server response
Avoid unnecessary messages when loading Firebrowse interface
Fix intron retention diagrams in distribution plots not displaying introns
When searching for specific splicing events, fix results based on the wrong genomic coordinates
psichomics 1.18.0 (18 May, 2021)
discardLowCoveragePSIvalues(): improve performance (2x faster)OrgDbdataplotSplicingEvent()directly with a PSI table to plot diagrams of the alternative splicing events withinplotDistribution()):typein command-line interface)subtitlein command-line interface)invertAxesin command-line interface)Bug fixes and minor changes
loadLocalFiles(): print elapsed time after loading local filesfilterGroups()was modified to return a character vector whose names are original names (instead of groups) and include an attribute Groups with the respective group of each value (together with their colour, if available):