heatmap.with.lgfold.riskpro: Plot heatmap with log 2 fold change and risk probability...

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Plot heatmap with log 2 fold change and risk probability information

Description

Plot heatmap with log 2 fold change and risk probability information

Usage

heatmap.with.lgfold.riskpro(
  heatmap.df,
  label,
  risk.pro = NA,
  lgfold = NA,
  scale = TRUE,
  group.name = "Cancer",
  bar.name = "Log2FC",
  ylim = c(0, 1),
  show.lgfold = TRUE,
  show.risk.pro = TRUE,
  height = 5,
  annotation.df = NULL,
  show_column_names = FALSE,
  show_row_names = TRUE,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  cluster_within_group = FALSE,
  z.score.cutoff = 2,
  specified.color = c("#0c3e74", "#77a8cd", "white", "#d86652", "#7e0821"),
  palette = "jama_classic"
)

Arguments

heatmap.df	Row: miRNA, Column: Sample
label	A factor with labels TURE/FALSE
lgfold	corresponded to row name sequence
scale	Default "TRUE"
group.name	Default "Cancer"
ylim	= c(0, 1), risk score range.
show.lgfold	= TRUE. Whether to show right panel.
annotation.df	Annotation data.frame
show_column_names	Default False
show_row_names	Defaut TRUE
cluster_within_group	Cluster within group
z.score.cutoff	Default 2
specified.color	Default c("#0c3e74","#77a8cd","white","#d86652","#7e0821") or colorRampPalette(c("navy", "white", "firebrick3"))(50)
palette	Color palette for group. Default "jama_classic"

Value

A heatmap plot by complex heatmap

Examples

heatmap.with.lgfold.riskpro(data.tmp[candi,],label, logfd,  risk.pro)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.