Heatmap for DEG data frame — enhance

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

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())