EnrichedView: View enriched terms

In MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Description

Grid plot for enriched terms

Usage

EnrichedView(
  enrichment,
  rank_by = "pvalue",
  mode = 1,
  subset = NULL,
  top = 0,
  bottom = 0,
  x = "LogFDR",
  charLength = 40,
  filename = NULL,
  width = 7,
  height = 4,
  ...
)

Arguments

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.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

See Also

EnrichedView

Examples

data(geneList, package = "DOSE")
## Not run: 
    enrichRes = enrich.GSE(geneList, organism="hsa")
    EnrichedView(enrichRes, top = 5, bottom = 5)

## End(Not run)

Example output

	11 genes are mapped ...
preparing geneSet collections...
GSEA analysis...
sh: 1: wc: Permission denied
no term enriched under specific pvalueCutoff...

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.