getPatternGeneSet: replace pathways column with gene.set #108
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Bug found in issue #107. Creating a separate column for "gene.set" apart from the "pathways" column generated by the fgsea and fora functions led to gene set names being associated with the wrong rows. To avoid this kind of issue of redundant columns naming the gene sets that caused this bug, the pathways column is renamed to gene.set then converted to a factor ordered by adjusted p-value.
Tests for gene set plotting now include a check for a sig_p1 gene set that should be associated with pattern 1.
dimalvovs
reviewed
May 29, 2024
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thank you for adding tests!
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Avoids redundant data frame column issue by renaming the "pathways" column to "gene.set" before converting this column to a factor ordered by adjusted p-value.