EnrichedView {MAGeCKFlute}R Documentation

View enriched terms

Description

Grid plot for enriched terms

Usage

EnrichedView(enrichment, rank_by = "p.adjust", top = 5, bottom = 5,
  custom_pid = NULL, x = "LogP", 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

"p.adjust" or "NES", specifying the indices for ranking pathways.

top

An integer, specifying the number of top enriched terms to show.

bottom

An integer, specifying the number of bottom enriched terms to show.

custom_pid

A character vector (pathway IDs), customizing pathways to show.

x

Character, "NES" or "LogP", 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

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

## End(Not run)

[Package MAGeCKFlute version 1.4.3 Index]