plot_by_grp: Make box, dot, violin or bar plots for a feature per group

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Make box, dot, violin or bar plots for a feature per group

Description

Make box, dot, violin or bar plotsfor a feature per group using ggplot2.

Usage

plot_by_grp(
  object,
  grp,
  name = "topgenes",
  width = 7,
  height = 7,
  main.v = "",
  xlab = "Group",
  ylab = "Log2 Expression",
  type = "dot",
  manual.color = NULL,
  x.angle = 0,
  add.se = FALSE,
  dotsize = 0.7,
  bins = 30,
  violin.alpha = 0.3,
  dot.alpha = 0.3,
  add.dot = FALSE,
  bar.width = 0.7,
  errorbar.width = 0.3
)

Arguments

object	Matrix-like object with features (e.g. genes) as rows and samples as columns.
grp	Vector of phenotype groups of the samples, which represent valid variable names in R. Should be same length as ncol(object). If the vector is named, names should match colnames(object).
name	Name of file to create. Set to NA to plot to screen instead of to file.
width	Manual option for determining the output file width in inches.
height	Manual option for determining the output file height in inches.
main.v	Character vector of main titles for plot.
xlab	Label for x-axis.
ylab	Label for y-axis.
type	Type of plot. Either "dot", "box", "violin", or "bar".
manual.color	Vector passed to both scale_fill_manual and scale_color_manual.
x.angle	Angle of x-axis text, passed to theme(axis.text.x=element_text(angle)).
add.se	Logical indicating if to add standard error of the mean to dot plot.
dotsize	Passed to geom_dotplot dotsize for dot plot.
bins	Used to calculate binwidth, which is passed to geom_dotplot binwidth for dot plot.
violin.alpha	Colour transparency in [0,1] for violin in violin plot.
dot.alpha	olour transparency in [0,1] for dots in violin plot.
add.dot	Logical indicating if to add individual data points as dots to bar plot.
bar.width	Width of the bars in bar plot.
errorbar.width	Width of the errorbars in bar plot.

Details

Based on type, "_dotplots", "_boxplots", "_violinplots", or "_barplots"is appended to name.

If object is a data frame, it is coerced to a matrix using data.matrix.

Value

Invisibly, a ggplot object from the last row of object that was plotted.

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.