DEGtopHeatmap: Heatmap for DEG data frame

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Heatmap for DEG data frame

Description

default will return a top 100 deg heatmap in p value = 0.05

Usage

DEGtopHeatmap(
  object,
  which,
  top = 50,
  filename = NA,
  show_gene = TRUE,
  category = "H",
  palette = RColorBrewer::brewer.pal(3, "Set2")[1:2],
  ...
)

Arguments

object	a counts data frame of rows in genes and columns in samples
which	which model of deg analysis. kinds of DEG; can be "limma", "edgeR", "DESeq2" or "MSigDB"
top	a single number or a length of 2 numeric vector, if 2 numeric vector, first one is top max logFC.
filename	NA or a file path
show_gene	logical,show gene name
category	MSigDB collection abbreviation, such as H or C1.
palette	a color palette for plots
...	More pheatmap parameters.

Value

a heatmap plot file

Examples

DEGtopHeatmap(object,which = "limma")

xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.