draw_volcano2: draw_volcano2

In tinyarray: Expression Data Analysis and Visualization

draw_volcano2

Description

print one or more volcano plot for Differential analysis result in data.frame fomat.

Usage

draw_volcano2(deg, pkg = 4, lab, ...)

Arguments

deg	a data.frame created by Differential analysis
pkg	a integer ,means which Differential analysis packages you used,we support three packages by now, 1,2,3,4 respectively means "DESeq2","edgeR","limma(voom)","limma"
lab	label for x axis in volcano plot, if NA , x axis names by package
...	other parameters from draw_volcano

Value

one or more volcano plot

Author(s)

Xiaojie Sun

See Also

geo_download;draw_volcano;draw_venn

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
#two group
gse = "GSE42872"
geo = geo_download(gse,destdir=tempdir())
group_list = rep(c("A","B"),each = 3)
ids = AnnoProbe::idmap('GPL6244',destdir = tempdir())
deg = get_deg(geo$exp,group_list,ids)
draw_volcano2(deg)
#multigroup
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$exp[1:4,1:4]
geo$exp=log2(geo$exp+1)
group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
find_anno(geo$gpl)
ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE,entriz = FALSE)
draw_volcano2(deg)
draw_volcano2(deg,color = c("darkgreen","grey","darkred"))
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

tinyarray documentation built on June 22, 2024, 9:58 a.m.