draw_boxplot: draw boxplot for expression

In tinyarray: Expression Data Analysis and Visualization

draw boxplot for expression

Description

draw boxplot for expression

Usage

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

Value

a boxplot according to exp and grouped by group.

Author(s)

Xiaojie Sun

See Also

draw_heatmap;draw_volcano;draw_venn

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')")
}
}

tinyarray documentation built on June 22, 2024, 9:58 a.m.