plot_box: Box Plots by Sample

In dswatson/bioplotr: Pretty, simple, optionally interactive plots for bioinformatics analysis pipelines

Box Plots by Sample

Description

This function displays each sample's omic data distribution as a box and whisker plot.

Usage

plot_box(
  dat,
  group = NULL,
  pal_group = "npg",
  type = NULL,
  ylab = NULL,
  title = "Box Plot",
  legend = "right",
  hover = FALSE
)

Arguments

dat	Omic data matrix or matrix-like object with rows corresponding to probes and columns to samples. Raw counts stored in DGEList or DESeqDataSet objects are automatically extracted and transformed to the log2-CPM scale, with a warning.
group	Optional character or factor vector of length equal to sample size. Numeric or logical vectors are silently coerced to factor. Levels are used to color box plots. If supplied, legend title defaults to "Group". Override this feature by passing a named list instead.
pal_group	String specifying the color palette to use if group is non-NULL, or a vector of such strings with length equal to the number of vectors passed to group. Options include "ggplot", all qualitative color schemes available in RColorBrewer, and the complete collection of ggsci palettes. Alternatively, a character vector of colors with length equal to the cumulative number of levels in group.
ylab	Optional label for y-axis.
title	Optional plot title.
legend	Legend position. Must be one of "bottom", "left", "top", "right", "bottomright", "bottomleft", "topleft", or "topright".
hover	Show sample name by hovering mouse over data point? If TRUE, the plot is rendered in HTML and will either open in your browser's graphic display or appear in the RStudio viewer.

Details

Box plots offer an intuitive way to visualize an omic data distribution. They are common in quality control pipelines, and may be especially helpful when contrasting pre- and post-normalization matrices. plot_box can additionally be used to inspect for batch effects or associations with phenotypic factors by using the group argument.

Examples

# Box plots by sample
mat <- matrix(rnorm(500 * 10), nrow = 500, ncol = 10)
plot_box(mat)

# Box plots by group
grp <- rep(c("A", "B"), each = 5)
plot_box(mat, group = grp)

dswatson/bioplotr documentation built on March 3, 2023, 9:43 p.m.