Af_distance_scatterplot: Function to scatterplot the distance to the germline to a...

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

Function to scatterplot the distance to the germline to a numerical node feature of the AntibodyForests-object

Description

Function to scatterplot the distance to the germline to a numerical node feature of the AntibodyForests-object

Usage

Af_distance_scatterplot(
  AntibodyForests_object,
  node.features,
  distance,
  min.nodes,
  color.by,
  color.by.numeric,
  correlation,
  geom_smooth.method,
  color.palette,
  font.size,
  ylabel,
  point.size,
  output.file
)

Arguments

AntibodyForests_object	AntibodyForests-object, output from Af_build()
node.features	Node features in the AntibodyForests-object to compare (needs to be numerical)
distance	string - How to calculate the distance to the germline. 'node.depth' : The sum of edges on the shortest parth between germline and each node 'edge.length' : The sum of edge length of the shortest path between germline and each node (Default)
min.nodes	The minimum number of nodes for a tree to be included in this analysis (this included the germline). Default is 2.
color.by	Color the scatterplot by a node.feature in the AntibodyForests-object, by the sample, or no color ("none). Default is "none".
color.by.numeric	Logical. If TRUE, the color.by feature is treated as a numerical feature. Default is FALSE.
correlation	"pearson", "spearman", "kendall", or "none"
geom_smooth.method	"none", lm" or "loess". Default is "none".
color.palette	The color palette to use for the scatterplot. Default for numerical color.by is "viridis".
font.size	The font size of the plot. Default is 12.
ylabel	The labels of the y-axis, in the same order as the node.features. Default is the node.features
point.size	The size of the points in the scatterplot. Default is 1.
output.file	string - specifies the path to the output file (PNG of PDF). Defaults to NULL.

Value

A ggplot2 object with the scatterplot

Examples

Af_distance_scatterplot(AntibodyForests_object = AntibodyForests::small_af,
                        node.features = "size",
                        distance = "edge.length",
                        min.nodes = 5,
                        color.by = "sample",
                        color.by.numeric = FALSE,
                        geom_smooth.method = "lm",
                        correlation = "pearson")

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