EnrichedGeneView {MAGeCKFlute} | R Documentation |
Visualize selected genes in enriched genesets
EnrichedGeneView(enrichment, geneList, keytype = "Symbol", gene_cutoff = c(-log2(1.5), log2(1.5)), top = 5, bottom = 5, charLength = 40, filename = NULL, width = 7, height = 5, ...)
enrichment |
A data frame of enrichment result. |
geneList |
The geneList used in enrichment analysis. |
keytype |
"Entrez" or "Symbol". |
gene_cutoff |
A tow-length numeric vector, specifying cutoff for negative and positive selections. |
top |
An integer, specifying the number of top enriched terms to show. |
bottom |
An integer, specifying the number of bottom enriched terms to show. |
charLength |
Integer, specifying max length of enriched term name to show as coordinate lab. |
filename |
Figure file name to create on disk. Default filename="NULL", which means no output. |
width |
As in ggsave. |
height |
As in ggsave. |
... |
Other available parameters in ggsave. |
An object created by ggplot
, which can be assigned and further customized.
Wubing Zhang
data(geneList, package = "DOSE") enrichRes <- enrich.GSE(geneList) EnrichedGeneView(enrichment=as.data.frame(enrichRes), geneList, keytype = "Entrez")