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]

# Plot violins of outdegree by sample
plotSubtrees(graphs, "SAMPLE", "out", main_title="Node outdegree", 
style="v")

2


# Plot violins of subtree by sample
plotSubtrees(graphs, "SAMPLE", "size", style="v")

4


# Plot boxplot of pathlength by isotype
plotSubtrees(graphs, "ISOTYPE", "path", colors=IG_COLORS, 
legend_title="Isotype", style="b")

Warning:The following are missing from the ‘colors’ argument and will be colored grey: IgA,IgG IgD,IgG7


# Plot boxplot of depth by isotype
plotSubtrees(graphs,  "ISOTYPE", "depth", style="b")

9

See also

Subtree statistics are calculated with summarizeSubtrees.