FastEnrichPlot: Fast way to draw enrich plot after clusterProfilter...

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

Fast way to draw enrich plot after clusterProfilter enrichfunction

Usage

FastEnrichPlot(object, pvalueCutoff = NULL, qvalueCutoff = NULL,
  id.col = "Description", select = NULL,
  x.title = "Biological Process terms", y.title = "-log10(FDR)",
  size = 15, short.cutoff = 46, topshow = 10)

Arguments

object	result from enrichGO or enrichKEGG or gseGO or enrichKEGG
pvalueCutoff	p value cutoff
qvalueCutoff	q value cutoff
id.col	ID you want to show in final plot
select	if select = NULL,the number of topshow would be shown.If select != NULL,selected terms would be showed and thus topshow is not effecient.
x.title	the title of x axis
y.title	the title of y axis
size	the size of whole plot
short.cutoff	if the number of character of terms is larger than short.cutoff,it would automatically change row in the showed plot.Defaut is 46.If you don't want change-row,just set short.cutoff = Inf
topshow	the number of top iterms ordered by FDR you want to show.It works only select = NULL

Value

LuckyList Object

Author(s)

Weibin Huang<[e-mail]>

Examples

## This is a simulative process and available only with CORRECT VARIABLES
load("E:/iProjects/LM_WGCNA/data/LM_WGCNA_02A/rda/goList.rda")
object <- goList$GOEnrichment$BP
res_EP <- FastEnrichPlot(object = object,
                         pvalueCutoff = NULL,
                         qvalueCutoff = NULL,
                         id.col = "Description",
                         select = NULL,
                         x.title = "Biological Process terms",
                         y.title = "-log10(FDR)",
                         size = 15,
                         short.cutoff = 46,
                         topshow = 10)
win.graph(12,9);res_EP$Plot

pvalueCutoff = 0.05
qvalueCutoff = 0.05
select = res2$ID[1:10]
id.col = "Description"
x.title = "Biological Process terms"
y.title = "-log10(FDR)"

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.