motif_plot: Code for plotting the Motif based on a specific CDR3 length...

In ClusTCR2: Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2'

Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for ).

Description

Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for ).

Usage

motif_plot(
  ClusTCR,
  Clust_column_name = "Clust_size_order",
  Clust_selected = NULL
)

Arguments

ClusTCR	Matrix file produce from mcl_cluster
Clust_column_name	Name of clustering column from mcl_cluster file e.g. cluster
Clust_selected	Select which cluster to display. Only one at a time.

Value

A ggplot object representing the motif.

Examples

# Example usage of mcl_cluster function with a stored file
example_file <- read.csv(system.file("extdata", "my_data.csv",package = "ClusTCR2"))
# Perform clustering using mcl_cluster function
step1 <- ClusTCR(example_file,allele = FALSE)
# perform mcl
step2 <- mcl_cluster(step1)
# print the motif plot for the simple clustering
print(motif_plot(step2,Clust_selected = 1))

ClusTCR2 documentation built on May 29, 2024, 9:32 a.m.