FastWGCNA_network: Visualize specified module Network after FastWGCNA pipeline

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

Description

Visualize specified module Network after FastWGCNA pipeline

Usage

FastWGCNA_network(object, module, hubGenes = NULL,
  hubGenes.color = mycolor[21], ratio = 0.8, size = 15,
  linkDistance = 300, linkWidth = 6, linkColour.type = NULL,
  opacityNoHover = 0, save.path = "WGCNA", names = "love")

Arguments

object	the result from FastWGCNA
module	module name.It must be a color oject like "blue"/"red"
hubGenes	Genes you want to highlight.Default is NULL,which means no gene would be highlighted.
hubGenes.color	the color of hubGenes.Default is mycolor[21].
ratio	The portion of data you select
size	a numeric to adjust the size of nodes
linkDistance	link distance
linkWidth	the width of link.If it is not a numeric,the default "JS(function(d) { return Math.sqrt(d.value); })" would be used.
linkColour.type	a list of link color for value mapping.
opacityNoHover	the legend intensity.From 0-1.Default is 0
save.path	the space of the save file.Default is "WGCNA"
names	part of saved files name

Examples

## NOT RUN
object = wgcna;rm(wgcna);
module = "blue"
hubGenes = c("ENSG00000009790","ENSG00000185811","ENSG00000134516","ENSG00000167613","ENSG00000122122","ENSG00000010610","ENSG00000066336","ENSG00000183813","ENSG00000102245","ENSG00000135426")

CoNet_moduleBlue <- FastWGCNA_network(object,
                                      module,
                                      hubGenes,
                                      ratio = 0.8,
                                      size = 15,
                                      linkDistance = 300,
                                      linkWidth=6,
                                      linkColour.type = NULL,
                                      opacityNoHover = 0,
                                      save.path = "WGCNA",
                                      names = "love")

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