plot_exposures: Display sample exposures with bar, box, or violin plots

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Display sample exposures with bar, box, or violin plots

Description

The distributions of mutational signatures can be viewed with barplots or box/violin plots. Barplots are most useful for viewing the proportion of signatures within and across samples. The box/violin plots are most useful for viewing the distributions of signatures with respect to sample annotations. Samples can be grouped using the group_by parameter. For barplots, various methods of sorting samples from left to right can be chosen using the sort_samples parameter.

Usage

plot_exposures(
  result,
  plot_type = c("bar", "box", "violin"),
  proportional = FALSE,
  group_by = "none",
  color_by = c("signature", "annotation"),
  annotation = NULL,
  num_samples = NULL,
  sort_samples = "total",
  threshold = NULL,
  same_scale = FALSE,
  add_points = FALSE,
  point_size = 2,
  label_x_axis = FALSE,
  legend = TRUE,
  plotly = FALSE
)

Arguments

result	A musica_result object generated by a mutational discovery or prediction tool.
plot_type	One of "bar", "box", or "violin". Default "bar".
proportional	If TRUE, then the exposures will be normalized to between 0 and 1 by dividing by the total number of counts for each sample. Default FALSE.
group_by	Determines how to group samples into the subplots (i.e. facets). One of "none", "signature" or "annotation". If set to "annotation", then a sample annotation must be supplied via the annotation parameter. Default "none".
color_by	Determines how to color the bars or box/violins. One of "signature" or "annotation". If set to "annotation", then a sample annotation must be supplied via the annotation parameter. Default "signature".
annotation	Sample annotation used to group the subplots and/or color the bars, boxes, or violins. Default NULL.
num_samples	The top number of sorted samples to display. If NULL, then all samples will be displayed. If group_by is set, then the top samples will be shown within each group. Default NULL.
sort_samples	This is used to change how samples are sorted in the barplot from left to right. If set to "total", then samples will be sorted from those with the highest number of mutation counts to the lowest (regardless of how the parameter "proportional" is set). If set to "name", then samples are sorted by their name with the mixedsort function. If set to one or more signature names (e.g. "Signature1"), then samples will be sorted from those with the highest level of that signature to the lowest. If multiple signatures are supplied then, samples will be sorted by each signature sequentially. Default "total".
threshold	Exposures less than this threshold will be set to 0. This is most useful when more than one signature is supplied to sort_samples as samples that are set to zero for the first exposure will then be sorted by the levels of the second exposure. Default NULL.
same_scale	If TRUE, then all subplots will have the same scale. Only used when group_by is set. Default FALSE.
add_points	If TRUE, then points for individual sample exposures will be plotted on top of the violin/box plots. Only used when plot_type is set to "violin" or "box". Default TRUE.
point_size	Size of the points to be plotted on top of the violin/box plots. Only used when plot_type is set to "violin" or "box" and add_points is set to TRUE. Default 2.
label_x_axis	If TRUE, x-axis labels will be displayed at the bottom of the plot. Default FALSE.
legend	If TRUE, the legend will be displayed. Default TRUE.
plotly	If TRUE, the the plot will be made interactive using plotly. Default FALSE.

Value

Generates a ggplot or plotly object

Examples

data(res_annot)
plot_exposures(res_annot, plot_type = "bar", annotation = "Tumor_Subtypes")

campbio/musicatk documentation built on July 14, 2024, 8:28 a.m.