richplot: richplot

Description Usage Arguments

View source: R/richplot.R

Description

plot the sigificant terms and shared genes with network format

Usage

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richplot(
  resultFis,
  top = 50,
  pvalue.cutoff = 0.05,
  padj.cutoff = NULL,
  usePadj = TRUE,
  useTerm = TRUE,
  low = "orange",
  high = "red",
  writeCyt = FALSE,
  cytoscapeFile = "network-file-for-cytoscape.txt",
  label.color = "black",
  label.size = 2,
  node.shape = NULL,
  layout = layout.fruchterman.reingold,
  savefig = FALSE,
  filename = "network",
  width = 7,
  height = 7,
  node.alpha = 0.7,
  repel = TRUE,
  segment.size = 0.2
)

Arguments

resultFis

Enrichment results

top

number of terms to show (default: 50)

pvalue.cutoff

cutoff p value for enrichment result

padj.cutoff

cutoff p adjust value for enrichment result

useTerm

use terms for nodes (default: TRUE)

low

color used for small value

high

color used for large value

writeCyt

write out the cytoscape file

cytoscapeFile

output cytoscape File

label.color

label color

label.size

label size

node.shape

shape of the node

layout

layout method

savefig

save figures or not

filename

output figure name

width

width for output figure

height

height for output figure

node.alpha

alpha-transparency scales

repel

use ggrepel text function or not

segment.size

segment size for ggrepel text


guokai8/Enrichr documentation built on May 16, 2020, 10:24 p.m.