Af_distance_boxplot: Function to make a grouped boxplot of distance between nodes...
In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

Af_distance_boxplot

R Documentation

Function to make a grouped boxplot of distance between nodes from specific groups and the germline of lineage trees constructed with AntibodyForests.

Description

Function to compare trees.

Usage

Af_distance_boxplot(
  AntibodyForests_object,
  distance,
  min.nodes,
  groups,
  node.feature,
  unconnected,
  colors,
  text.size,
  x.label,
  group.order,
  significance,
  parallel,
  output.file
)

Arguments

`AntibodyForests_object`	AntibodyForests-object, output from Af_build()
`distance`	string - How to calculate the distance to the germline. 'node.depth' : Average of the sum of edges on the shortest parth between germline and nodes from this group. 'edge.length' : Average of the sum of edge length of the shortest path between germline and nodes from this group. (Default)
`min.nodes`	The minimum number of nodes for a tree to be included in this analysis (this included the germline)
`groups`	Which groups to compare. These groups need to be in the node features of the AntibodyForests-object. Set to NA if all features should displayed. (default is NA) If you want to compare IgM and IgG for example, groups should be c("IgM, "IgG") (not "Isotypes")
`node.feature`	Node feature in the AntibodyForests-object to compare.
`unconnected`	If TRUE, trees that don't have all groups will be plotted, but not included in significance analysis. (default FALSE)
`colors`	Optionally specific colors for the group (Will be matched to the groups/names on alphabetical order).
`text.size`	Font size in the plot (default 20).
`x.label`	Label for the x-axis (default is the node feature).
`group.order`	Order of the groups on the x-axis. (default is alphabetical/numerical)
`significance`	If TRUE, the significance of the difference (paired t-test) between the groups is plotted. (default FALSE)
`parallel`	If TRUE, the metric calculations are parallelized across clonotypes. (default FALSE)
`output.file`	string - specifies the path to the output file (PNG of PDF). Defaults to NULL.

Value

A ggplot2 object with the boxplot.

Examples

Af_distance_boxplot(AntibodyForests::small_af,
                    distance = "edge.length",
                    min.nodes = 5,
                    groups = c("IGHA", "IgG1"),
                    node.feature = "isotype",
                    unconnected = TRUE)

AntibodyForests documentation built on April 4, 2025, 4:45 a.m.