ggnetwork_internal | R Documentation |
generate network based on Enrichment results
network for Enrichment results
network for Enrichment results
network for Enrichment results
ggnetwork_internal(
object = object,
gene = gene,
top = 50,
pvalue = 0.05,
padj = NULL,
usePadj = TRUE,
low = "orange",
high = "red",
weightcut = 0.2,
useTerm = TRUE,
writeCyt = FALSE,
cytoscapeFile = NULL,
cytoscapeFormat = "graphml",
label.color = "black",
label.size = 2,
node.shape = NULL,
layout = "fruchtermanreingold",
savefig = FALSE,
visNet = FALSE,
smooth = TRUE,
nodeselect = FALSE,
edit = FALSE,
savehtml = FALSE,
filename = NULL,
width = 7,
height = 7,
segment.size = 0.2,
node.alpha = 0.7,
sep = ",",
...
)
## S4 method for signature 'richResult'
ggnetwork(
object,
gene,
top = 50,
pvalue = 0.05,
padj = NULL,
usePadj = TRUE,
low = "orange",
high = "red",
weightcut = 0.2,
useTerm = TRUE,
writeCyt = FALSE,
cytoscapeFile = NULL,
cytoscapeFormat = "graphml",
label.color = "black",
label.size = 2,
node.shape = NULL,
layout = "fruchtermanreingold",
savefig = FALSE,
visNet = FALSE,
smooth = TRUE,
nodeselect = FALSE,
edit = FALSE,
savehtml = FALSE,
filename = NULL,
width = 7,
height = 7,
segment.size = 0.2,
node.alpha = 0.7,
sep = ",",
...
)
## S4 method for signature 'data.frame'
ggnetwork(
object,
gene = NULL,
top = 50,
pvalue = 0.05,
padj = NULL,
usePadj = TRUE,
low = "orange",
high = "red",
weightcut = 0.2,
useTerm = TRUE,
writeCyt = FALSE,
cytoscapeFile = NULL,
cytoscapeFormat = "graphml",
label.color = "black",
label.size = 2,
node.shape = NULL,
layout = "fruchtermanreingold",
savefig = FALSE,
visNet = FALSE,
smooth = TRUE,
nodeselect = FALSE,
edit = FALSE,
savehtml = FALSE,
filename = NULL,
width = 7,
height = 7,
segment.size = 0.2,
node.alpha = 0.7,
sep = ",",
...
)
## S4 method for signature 'GSEAResult'
ggnetwork(
object,
gene,
top = 50,
pvalue = 0.05,
padj = NULL,
usePadj = TRUE,
low = "orange",
high = "red",
weightcut = 0.2,
useTerm = TRUE,
writeCyt = FALSE,
cytoscapeFile = NULL,
cytoscapeFormat = "graphml",
label.color = "black",
label.size = 2,
node.shape = NULL,
layout = "fruchtermanreingold",
savefig = FALSE,
visNet = FALSE,
smooth = TRUE,
nodeselect = FALSE,
edit = FALSE,
savehtml = FALSE,
filename = NULL,
width = 7,
height = 7,
segment.size = 0.2,
node.alpha = 0.7,
sep = ",",
...
)
object |
data.frame object |
gene |
vector contains gene names or dataframe with DEGs information |
top |
number of terms to display |
pvalue |
cutoff value of pvalue (if padj set as NULL) |
padj |
cutoff value of p adjust value |
usePadj |
use p adjust value as color or not (should use with padj) |
low |
color used for small value |
high |
color used for large value |
weightcut |
cutoff valule for edge |
writeCyt |
write out the cytoscape file |
cytoscapeFile |
output cytoscape File |
cytoscapeFormat |
Character string giving the output file format |
label.color |
label color |
label.size |
label size |
layout |
layout method ('fruchtermanreingold','kamadakawai','target','circle') |
savefig |
save the figure or not |
filename |
figure output name |
width |
figure width |
height |
figure height |
segment.size |
size for label segment |
node.alpha |
alpha-transparency scales |
sep |
character string used to separate the genes when concatenating |
label.font |
label font |
Kai Guo
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