GSEA analyses NES plotter. Plotting of a bar plot indicating the Normalized Enrichment Score (NES) of a gsea result. Bars will have different colors by positive or negative enrichment and transparency proportional to their p-value.
NES.plot(
enrichResult,
pos.NES.label = "+NES",
neg.NES.label = "-NES",
pos.NES.color = "steelblue",
neg.NES.color = "orange",
string.pattern.to.remove = "HALLMARK|GOBP",
alpha.range = c(0.3, 1),
add.counts = TRUE,
perc.bleeding.x = 8,
axes.text.size = 10,
title = "NES enrichments"
)A DEprot.enrichResult object, as generated by geneset.enrichment DEprot function, or a gseaResult object as generate by clusterprofiler.
String for the label of sets enriched in the group with positive ranking feature scores. Default: "+NES".
String for the label of sets enriched in the group with negative ranking feature scores. Default: "-NES".
String for the color of sets enriched in the group with positive ranking feature scores. Default: "steelblue".
String for the color of sets enriched in the group with negative ranking feature scores. Default: "orange".
String with a regular expression of a pattern to be removed from the set names. Default: "HALLMARK|GOBP".
Numeric vector of length 2 indicating minimum and maximum value for the transparency. Individual values must be a number between 0 and 1. Default: c(0.3, 1).
Logic value to indicate whether add labels with the set size counts. Default: "TRUE".
Numeric value indicating the percentage of the full x.axis range to add on the left on the right. Useful when labels are falling outside for the x-max. Default: 8 (%).
Numeric value indicating the font size of the axis text. Default: 10.
String indicating the title of the plot. Default: "NES enrichments".
A ggplot object.