draw_boxplot function

draw boxplot for expression

draw_boxplot(
  exp,
  group_list,
  method = "kruskal.test",
  sort = TRUE,
  drop = FALSE,
  width = 0.5,
  pvalue_cutoff = 0.05,
  xlab = "Gene",
  ylab = "Expression",
  grouplab = "Group",
  p.label = FALSE,
  add_error_bar = FALSE,
  color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#66C2A5", "#FC8D62", "#8DA0CB",
    "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  ...
)

Arguments

• exp: A numeric matrix
• group_list: A factor with duplicated character or factor
• method: one of kruskal.test,aov,t.test and wilcox.test
• sort: whether the boxplot will be sorted
• drop: whether to discard insignificant values
• width: width of boxplot and error bar
• pvalue_cutoff: if drop = TRUE,genes with p-values below the threshold will be drawn
• xlab: title of the x axis
• ylab: title of the y axis
• grouplab: title of group legend
• p.label: whether to show p value in the plot
• add_error_bar: whether to add error bar
• color: color vector
• ...: other parameters from stat_compare_means

Returns

a boxplot according to exp and grouped by group.

Examples

if(requireNamespace("tidyr",quietly = TRUE)&
   requireNamespace("ggpubr",quietly = TRUE)){
  draw_boxplot(t(iris[,1:4]),iris$Species)
  exp <-  matrix(rnorm(60),nrow = 10)
  colnames(exp) <- paste0("sample",1:6)
  rownames(exp) <- paste0("gene",1:10)
  exp[,4:6] = exp[,4:6] +10
  exp[1:4,1:4]
  group_list <- factor(rep(c("A","B"),each = 3))
  draw_boxplot(exp,group_list)
  draw_boxplot(exp,group_list,color = c("grey","red"))
  }else{
if(!requireNamespace("ggpubr",quietly = TRUE)) {
 warning("Package 'ggpubr' needed for this function to work.
        Please install it by install.packages('ggpubr')")
}
if(!requireNamespace("tidyr",quietly = TRUE)) {
 warning("Package 'tidyr' needed for this function to work.
        Please install it by install.packages('tidyr')")
}
}

See Also

draw_heatmap;draw_volcano;draw_venn

Author(s)

Xiaojie Sun