R: Plots subtree statistics for multiple trees

plotSubtrees {alakazam} | R Documentation

## 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", "out", style="v")

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

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

[Package alakazam version 0.3.0 Index]