enhance_heatmap: Heatmap for DEG data frame

In xiayh17/RNAseqStat: 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

enhance_heatmap(
  counts_data,
  deg_data,
  group_list,
  x,
  y,
  top = 50,
  cut_P = 0.05,
  dir = ".",
  prefix = "2-DEG",
  palette = RColorBrewer::brewer.pal(3, "Set2")[1:2]
)

Arguments

counts_data	a counts data frame of rows in genes and columns in samples
deg_data	a DEG data frame contains logFC and p value
group_list	a character vector ordered by samples in counts_data
x	which column is log FC
y	which column is P value
top	a single number or a length of 2 numeric vector, if 2 numeric vector, first one is top max logFC.
cut_P	threshold value of P value, can set for every cut_FC number in numeric vector format
dir	a directory to store results
prefix	a prefix of file names in this step
palette	a color palette for plots

Value

a heatmap plot file

Examples

enhance_heatmap(counts_input, DEG_df, group_list,
    x = "log2FoldChange", y = "pvalue", dir = tempdir())

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.