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Show boxplots for columns of data in a matrix

Source: R/plot-boxplot2.R
plot_boxplot2.Rd

This is an alternative to plot_boxplot() using base R. This function should work with most matrix or matrix-like objects (which is especially useful for DelayedArray objects). The function also includes an option for computing the relative-log-expression of the input data, given the input data is on the log-scale.

Usage

plot_boxplot2(
  x,
  metadata = NULL,
  fill_by = NULL,
  rle = FALSE,
  hcl_palette = "Dark 3",
  plot_title = NULL,
  x_label = NULL,
  y_label = NULL,
  show_outliers = TRUE,
  show_legend = TRUE,
  legend_position = "top",
  legend_horiz = TRUE,
  legend_cex = 0.8,
  legend_ncol = 1,
  ...
)

Arguments

x

feature x sample matrix or matrix-like object.

metadata

data.frame containing metadata per sample. rownames of metadata must match the colnames of the input matrix. Default NULL, each sample in the matrix will be plotted.

fill_by

metadata column used to color boxplots by the grouping variable. Default NULL, each sample in the matrix will be plotted

rle

should the relative-log-expression value be plotted. Requires input matrix to be on the log-scale. Default = FALSE

hcl_palette

color palette applied to 'fill_by' variable. One of the hcl.pals(). Default "Dark 3"

plot_title

title of the plot. Default NULL

x_label

title of th x-axis. Default NULL

y_label

title of the y-axis. Default NULL

show_outliers

should boxplot outliers be shown. Default TRUE

show_legend

should the legend be drawn on the plot when fill_by is set? Default TRUE

legend_position

location keyword for the legend. One of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". Default "topright"

legend_horiz

logical; if TRUE, set the legend horizontally rather than vertically. Default TRUE

legend_cex

character expansion factor for legend text relative to current par. Default 0.8

legend_ncol

number of columns to set the legend items. Default 1. This is not used if legend_horiz=TRUE

...

additional arguments passed to bxp()

Value

boxplots of the column data

Examples


# Create metadata for plotting
metadata <- data.frame(row.names = colnames(GSE161650_lc))
metadata$Group <- rep(c("DMSO", "THZ1"), each = 3)

# Plot the boxplot by sample
plot_boxplot2(GSE161650_lc)


# Plot the boxplot by coloring each Group and transforming values
#  to relative-log-expression
plot_boxplot2(
  GSE161650_lc,
  metadata,
  fill_by = "Group",
  rle = TRUE,
  plot_title = "Relative log-expression",
  y_label = "RLE",
  show_outliers = FALSE
  )