Af_node_size_boxplot: Function to make a grouped boxplot of the normalized average...

In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

Function to make a grouped boxplot of the normalized average node sizes (number of cells with the exact same sequence) from specific groups of lineage trees constructed with AntibodyForests.

Description

Function to compare trees.

Usage

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

Arguments

AntibodyForests_object	AntibodyForests-object, output from Af_build()
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.
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_node_size_boxplot(AntibodyForests::small_af,
                    min.nodes = 5,
                    groups = c("IGHA", "IgG1"),
                    node.feature = "isotype")

AntibodyForests documentation built on Aug. 8, 2025, 6:49 p.m.