tinyarray (version 2.4.3)

plot_deg: plot_deg

Description

plot pca plot,volcano plot,heatmap,and venn plot for Differential analysis result

Usage

plot_deg(
  exp,
  group_list,
  deg,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  pvalue_cutoff = 0.05,
  logFC_cutoff = 1,
  adjust = FALSE,
  annotation_legend = FALSE,
  lab = NA,
  species = "human"
)

Value

plots

Arguments

exp

A numeric matrix

group_list

A factor with duplicated character or factor

deg

result of multi_deg or get_deg function

symmetry

a logical value ,would you like to get your plot symmetrical

my_genes

genes for pheatmap

show_rownames

boolean specifying if column names are be shown.

cluster_cols

boolean values determining if columns should be clustered or hclust object.

color_volcano

color for volcano

pvalue_cutoff

Cutoff value of pvalue,0.05 by default.

logFC_cutoff

Cutoff value of logFC,1 by default.

adjust

a logical value, would you like to use adjusted pvalue to draw this plot,FAlSE by default.

annotation_legend

boolean value showing if the legend for annotation tracks should be drawn.

lab

label for x axis in volcano plot, if NA , x axis names by package

species

choose human or mouse, or rat, default: human

Author

Xiaojie Sun

Examples

if (FALSE) {
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
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$gpl,destdir = tempdir())
deg = get_deg(geo$exp,group_list,ids,adjust = FALSE,entriz = FALSE)
plot_deg(geo$exp,group_list,deg)
}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)
  }
}
}