plotSubtrees: Plots subtree statistics for multiple trees

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Plots subtree statistics for multiple trees

Description

plotSubtree plots distributions of normalized subtree statistics for a set of lineage trees, broken down by annotation value.

Usage

plotSubtrees(
  graphs,
  field,
  stat,
  root = "Germline",
  exclude = c("Germline", NA),
  colors = NULL,
  main_title = "Subtrees",
  legend_title = "Annotation",
  style = c("box", "violin"),
  silent = FALSE,
  ...
)

Arguments

graphs	list of igraph objects containing annotated lineage trees.
field	string defining the annotation field.
stat	string defining the subtree statistic to plot. One of: outdegree: distribution of normalized node outdegrees. size: distribution of normalized subtree sizes. depth: distribution of subtree depths. pathlength: distribution of maximum pathlength beneath nodes.
root	name of the root (germline) node.
exclude	vector of strings defining field values to exclude from plotting.
colors	named vector of colors for values in field, with names defining annotation names field column and values being colors. Also controls the order in which values appear on the plot. If NULL alphabetical ordering and a default color palette will be used.
main_title	string specifying the plot title.
legend_title	string specifying the legend title.
style	string specifying the style of plot to draw. One of: "histogram": histogram of the annotation count distribution with a red dotted line denoting the observed value. "cdf": cumulative distribution function of annotation counts with a red dotted line denoting the observed value and a blue dotted line indicating the p-value.
silent	if TRUE do not draw the plot and just return the ggplot2 object; if FALSE draw the plot.
...	additional arguments to pass to ggplot2::theme.

Value

A ggplot object defining the plot.

See Also

Subtree statistics are calculated with summarizeSubtrees.

Examples

# Define example tree set
graphs <- ExampleTrees[1:10]

# Violin plots of node outdegree by sample
plotSubtrees(graphs, "sample_id", "out", style="v")

# Violin plots of subtree size by sample
plotSubtrees(graphs, "sample_id", "size", style="v")

# Boxplot of node depth by isotype
plotSubtrees(graphs, "c_call", "depth", style="b")

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.