draw_heatmap function

draw a heatmap plot

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

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

Returns

a heatmap plot according to exp and grouped by group.

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))
if(requireNamespace("ggplotify",quietly = TRUE)){
  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") )
}else{
  warning("Package 'ggplotify' needed for this function to work.
    Please install it by install.packages('ggplotify')")
}

See Also

draw_pca;draw_volcano;draw_venn

Author(s)

Xiaojie Sun