plot_deg: plot_deg

In tinyarray: Expression Data Analysis and Visualization

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"
)

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

Value

plots

Author(s)

Xiaojie Sun

Examples

## Not run: 
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)
plot_deg(geo$exp,group_list,deg)

## End(Not run)

tinyarray documentation built on Aug. 18, 2023, 9:07 a.m.