plot_partitioned_pc: Plot partitioned principal component

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Plot partitioned principal component

Description

Create a histogram and boxplot with per sample principal component values partitioned by a categorical variable.

Usage

plot_partitioned_pc(
  data,
  pc = 1,
  group_var,
  center = T,
  scale = T,
  feature_ids = NULL,
  sample_ids = NULL,
  invert_rows = F,
  invert_cols = F,
  return_data = F,
  binsize = NULL,
  colors = NULL,
  hist_alpha = 0.75,
  box_fill = "gray50",
  box_alpha = 0.5,
  box_lwd = 1,
  jitter_alpha = 0.5,
  jitter_size = 1.75,
  x_title = NULL,
  y_title = "Sample count"
)

Arguments

data	A SummarizedExperiment-like object. Must be compatible with assay() and colData().
pc	An integer for the principal component (ranked from highest to lowest variance contribution) to use for plotting.
group_var	A string for the categorical variable to use for partitioning.
center	A logical. Should the data be zero-centered prior to PCA?
scale	A logical. Should the data be scaled to unit variance prior to PCA?
feature_ids	A vector of row names for subsetting data for plotting.
sample_ids	A vector of column names for subsetting data for plotting.
invert_rows	A logical. Should feature_ids be used for excluding rows from plotting instead?
invert_cols	A logical. Should sample_ids be used for excluding columns from plotting instead?
return_data	A logical. Should plot data be returned instead of a ggplot object?
binsize	A numeric value for the histogram bin widths.
colors	A string vector. The histogram bar colors and jitter colors for each categorical variable value.
hist_alpha	A numeric value for the alpha level for histogram bars.
box_fill	A string. The fill color for the boxplot.
box_alpha	A numeric value for the alpha level for the boxplot.
box_lwd	A numeric value for the boxplot line width.
jitter_alpha	A numeric for the alpha level for jittered data points.
jitter_size	A numeric for the point size for jittered data points.
x_title	A string denoting the x-axis title. Only added to the boxplot.
y_title	A string denoting the y-axis title. Only added to the histogram.

Details

Runs PCA using a user-specified set of expression features (e.g., genes) and plots a user-specified PC as a histogram and boxplot. The two plots are intended to be used as a single column, two row figure panel. Data points in the plots are partitioned by a categorical variable.

Value

A list with two ggplot objects hist and boxplot corresponding to a histogram and jittered boxplot respectively. If return_data is TRUE, then a data frame with the plot data values and grouping variable.

See Also

hist_boxplot2 prcomp

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.