gg_boxplot: Boxplot with ggplot2

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

Boxplot with ggplot2

Description

Boxplot with ggplot2

Usage

gg_boxplot(
  data.tb,
  x.c = "",
  y.c = "",
  color.c = "",
  title.c = NA,
  xlab.c = NA,
  ylab.c = "",
  label.vc = "",
  palette.vc = "Set1",
  size.ls = list(dot.n = 0.7, lab.i = 20, tick.i = 20, title.i = 20),
  figure.c = c("interactive", "my_boxplot.pdf")[1]
)

Arguments

data.tb	Data frame (or tibble) containing the information
x.c	Character: name of the column with qualitative levels
y.c	Character: name of the column with quantitative values
color.c	Character: optional name of the column for color information
title.c	Character: plot title
xlab.c	Character: x label
ylab.c	Character: y label
label.vc	Character (vector): either the name of a character column from the data or a character vector of the same length as the rown number of the data, containing the feature labeling for outlier display
palette.vc	Character: either the name of an RColorBrewer palette (default: 'Set1'; 'Paired' can be useful for parallel plotting) or a vector manually defining the colors
size.ls	List of sizes for dots (default is 0.7), labels (default is 16), ticks (14) and title (20)
figure.c	Character: either 'interactive' for interactive display or 'my_barplot.pdf' for figure saving (only the extension matters)

Value

character vector of outlier labels (same dimension as the number of rows from data.tb)

Examples

sacurine.eset <- phenomis::reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
sacurine_pda.df <- Biobase::pData(sacurine.eset)
sacurine_pda.df <- sacurine_pda.df[!grepl("QC", rownames(sacurine_pda.df)), ]
phenomis::gg_boxplot(sacurine_pda.df, y.c = "age")
phenomis::gg_boxplot(sacurine_pda.df, x.c = "gender", y.c = "bmi", color.c = "gender")
phenomis::gg_boxplot(sacurine_pda.df, x.c = "gender", y.c = "bmi", color.c = "gender", label.vc = rownames(sacurine_pda.df))

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.