Plots an upset-plot for differential expression results
# S3 method for class 'upset'
plot(
DEprot.analyses.object,
contrast.subset = NULL,
title = NULL,
subtitle = NULL,
sort.intersections = "cardinality",
sort.sets = "descending",
intersection.bar.color = "black",
setsize.bar.color = "black",
show.counts = TRUE,
min.size = 1,
height.ratio = 0.5,
width.ratio = 0.3,
use.uncorrected.pvalue = FALSE
)An object of class DEprot.analyses.
Numeric vector indicating the contrasts to use. Default: NULL (all contrasts are shown).
String indicating the title to display. Markdown-mode supported. Default: NULL (no title).
String indicating the title to display. Markdown-mode supported. Default: NULL (subtitle).
String indicating which method to use for the intersection sorting: 'cardinality' or 'degree'. Default: "cardinality".
String indicating which method to use for the sets sorting: 'descending' or 'ascending'. Default: "descending".
String indicating the color to use for the intersection size bar plot. Default: "black".
String indicating the color to use for the set size bar plot. Default: "black".
Logical value indicating whether the counts in the intersection bar pot should be shown. Default: TRUE.
Numeric value indicating the minimal number of interactions to show. Default: 1.
Numeric value indicating the ratio of the intersection matrix to intersection size height. Default: 0.5.
Numeric value indicating the ratio of the overall set size width to intersection matrix width. Default: 0.3.
Logical value indicating whether it should be used the normal p-value instead of the adjusted one (differential proteins numbers are recomputed). Default: FALSE, padj is used.
A DEprot.upset with the upset plot and the matrix of the observed enriched proteins.