EnrichedView {MAGeCKFlute} | R Documentation |
Grid plot for enriched terms
EnrichedView( enrichment, rank_by = "pvalue", mode = 1, subset = NULL, top = 0, bottom = 0, x = "LogFDR", charLength = 40, filename = NULL, width = 7, height = 4, ... )
enrichment |
A data frame of enrichment result, with columns of ID, Description, p.adjust and NES. |
rank_by |
"pvalue" or "NES", specifying the indices for ranking pathways. |
mode |
1 or 2. |
subset |
A vector of pathway ids. |
top |
An integer, specifying the number of upregulated terms to show. |
bottom |
An integer, specifying the number of downregulated terms to show. |
x |
Character, "NES", "LogP", or "LogFDR", indicating the variable on the x-axis. |
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". |
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") ## Not run: enrichRes = enrich.GSE(geneList, organism="hsa") EnrichedView(enrichRes, top = 5, bottom = 5) ## End(Not run)