plotSubtrees - 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.

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")

See also¶

Subtree statistics are calculated with summarizeSubtrees.