draw_heatmap: draw a heatmap plot

In tinyarray: Expression Data Analysis and Visualization

draw a heatmap plot

Description

print a heatmap plot for expression matrix and group by group_list praramter, exp will be scaled.

Usage

draw_heatmap(
  n,
  group_list,
  scale_before = FALSE,
  n_cutoff = 3,
  legend = FALSE,
  show_rownames = FALSE,
  annotation_legend = FALSE,
  split_column = FALSE,
  show_column_title = FALSE,
  color = (grDevices::colorRampPalette(c("#2fa1dd", "white", "#f87669")))(100),
  color_an = c("#2fa1dd", "#f87669", "#e6b707", "#868686", "#92C5DE", "#F4A582",
    "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494",
    "#B3B3B3"),
  scale = TRUE,
  main = NA,
  ...
)

Arguments

n	A numeric matrix
group_list	A factor with duplicated character or factor
scale_before	deprecated parameter
n_cutoff	3 by defalut , scale before plot and set a cutoff,usually 2 or 1.6
legend	logical,show legend or not
show_rownames	logical,show rownames or not
annotation_legend	logical,show annotation legend or not
split_column	split column by group_list
show_column_title	show column title or not
color	color for heatmap
color_an	color for column annotation
scale	logical,scale the matrix or not
main	the title of the plot
...	other parameters from pheatmap

Value

a heatmap plot according to exp and grouped by group.

Author(s)

Xiaojie Sun

See Also

draw_pca;draw_volcano;draw_venn

Examples

#example data
exp = matrix(abs(rnorm(60,sd = 16)),nrow = 10)
exp[,4:6] <- exp[,4:6]+20
colnames(exp) <- paste0("sample",1:6)
rownames(exp) <- paste0("gene",1:10)
exp[1:4,1:4]
group_list = factor(rep(c("A","B"),each = 3))
draw_heatmap(exp,group_list)
#use iris
n = t(iris[,1:4]);colnames(n) = 1:150
group_list = iris$Species
draw_heatmap(n,group_list)
draw_heatmap(n,group_list,color = colorRampPalette(c("green","black","red"))(100),
             color_an = c("red","blue","pink") )

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