Version 1.12

psichomics 1.12.1 (29 January, 2020)

• Alternative splicing events can now be represented via diagrams:
  • Redesign of alternative splicing event selection (graphical interface)
  • plotSplicingEvent() plots diagram representation of alternative splicing events
  • In the visual interface, alternative splicing event diagrams were added below distribution plots (to quickly illustrate higher and lower values of alternative splicing quantification) and in annotation page
• User-provided junction quantification loading:
  • Support junction coordinates from mitochondrial, Z and W chromosomes
  • Fix issues with files containing splice junctions within random, alt and unknown chromosomes by discarding those rows (a warning is raised)
• Alternative splicing annotation:
  • listSplicingAnnotations() can now be filtered by species, assembly and data of available annotations
• Improve import/export of data groups from/to a file, including colour support
• Copy-edit and improve all tutorials, welcome message and help tab
• Include link to article in Methods in Molecular Biology: https://doi.org/10.1007/978-1-0716-0301-7_10

More bug fixes and minor changes

• TCGA and SRA data loading:
  • loadFirebrowseData() now returns expected data when asking for multiple datasets (such as in the case of performing a pan-cancer analysis) in both visual and command-line interface
  • SRA projects containing only one column of extra information in sample metadata are now correctly loaded instead of raising an error (loadSRAproject())
• Data loading and manipulation:
  • Copy-edit information on the format of user-provided files
  • Warn when discarding rows with duplicated rownames after loading user-provided files
  • getGtexDataTypes() is now exported, as expected
  • parseSplicingEvent() now returns the coordinates as numeric if coords = TRUE and char = FALSE
  • Improve dialog when trying to load a local folder without any supported files available
• Alternative splicing annotation:
  • Confirmation dialog is not displayed any more when creating a folder (specially useful while running the visual interface)
  • Allow to select cache directory of AnnotationHub (command-line interface)
  • Fix prepareGeneQuant() discarding the argument strandedness if either stranded or stranded (reverse)
• Data grouping:
  • Samples not associated with any subject are now kept when exporting groups to a file
  • Fix issues related with importing groups based on a file with groups of splicing events and/or genes
  • Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process
  • Show number of genes contained in pre-made gene lists
  • Discard unavailable genes when creating group of genes based on pre-made gene lists (unless these are automatically created at startup)
• Density plot (plotDistribution()):
  • Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn)
  • After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series)
  • Rug plot labels now show data values if sample names are not provided
  • Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values)
  • Fix misguiding example in function documentation
  • When hovering the values in the rug plot, the colour of the tooltip is now the same used for the rug points as expected
• Survival analysis (p-value plot):
  • Fix alternative splicing quantification cutoff being selected based on the one whose difference has the highest (instead of the lowest) p-value
  • Fix plot line label presenting “p < 0.05” independently of the threshold used for significance
• Gene, transcript and protein annotation:
  • Show available annotation information and query PubMed even if Ensembl is down
  • Avoid app crash when searching for PubMed articles too many times
• Improve warning/error alerts:
  • Fix alerts crashing the visual interface
  • Improve message formatting regarding HTML-containing alerts
• Improve unit tests and function documentation