ggnetplot,richResult-method | R Documentation |
richplot for Enrichment results
## S4 method for signature 'richResult'
ggnetplot(
object,
top = 50,
pvalue = 0.05,
padj = 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 = "fruchtermanreingold",
savefig = FALSE,
filename = "network",
width = 7,
height = 7,
node.alpha = 0.7,
repel = TRUE,
segment.size = 0.2,
sep = ","
)
object |
richResult or dataframe |
top |
number of terms to show (default: 50) |
pvalue |
cutoff p value for enrichment result |
padj |
cutoff p adjust value for enrichment result |
usePadj |
use adjust p value for the color or not |
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 ('fruchtermanreingold','kamadakawai','target','circle') |
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 |
sep |
character string used to separate the genes when concatenating |
Kai Guo
## Not run:
hsago<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
gene=sample(unique(hsago$GeneID),1000)
res<-richKEGG(gene,kodata = hsako)
ggnetplot(res)
## End(Not run)
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