Clonal Analysis Utilities in APackOfTheClones

In APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

knitr::opts_chunk$set(echo = FALSE)
options(repos = c(CRAN = "http://cran.rstudio.com"))

quiet_load_all_CRAN <- function(...) {
  for (pkg in list(...)) {
    if (require(pkg, quietly = TRUE, character.only = TRUE)) next
    invisible(install.packages(
      pkg, quiet = TRUE, verbose = FALSE, character.only = TRUE
    ))
    suppressPackageStartupMessages(invisible(
      require(pkg, quietly = TRUE, character.only = TRUE)
    ))
  }
}

# load packages
quiet_load_all_CRAN("ggplot2", "Seurat", "dplyr", "APackOfTheClones")

# load data
pbmc <- get(data("combined_pbmc"))

Introduction

Here is a small collection of potentially useful functions to modify clonal expansion plots and work with clonal data that may be relevant.

Seperately Modifying the Clone Size Legend

The removeLegend and overlayLegend functions both takes in an existing APackOfTheClones plot to either remove or change its position/aesthetics on the plot by directly modifying the ggplot object.

Getting Clone Sizes as a List

scRepertoire counts and store the clone sizes in a column of the seurat object metadata. The countCloneSizes function returns this information in a list where each element is a table object corresponding to the clonotype frequencies for that cluster, and a cluster with no clonotypes will have an empty table at its index. Alternatively, it can also get the aggregate clone sizes. It also allows for the same filtering arguments as seen in RunAPOTC() and vizAPOTC().

Getting Clonotypes Common Across Seurat Clusters

The getSharedClones is a convenience function does this with the subsetting arguments, and returns the shared clonotypes as a named list where the names are the clonotypes and the elements are numeric vectors where each number is one of the clusters that the clonotype name at its index correspond to. A combined seurat object is loaded with the variable name pbmc::

getSharedClones(pbmc, clonecall = "aa")

Getting Geometric Centroids For Seurat Reductions

The getReductionCentroids function is a shortcut for getting the centroids as a list of numeric vectors of length 2 based on some existing reduction in a seurat object.

head(getReductionCentroids(pbmc, "umap"))

Highlighting Specific Clonotypes

The scRepertoire package has a function scRepertoire::highlightClones that highlights specific points in the dimensional reduction plot that correspond to user clonotype inputs and darkening everything else. showCloneHighlight is the APackOfTheClones equivalent that does so for each clonotype circle:

showCloneHighlight(
    apotc_ggplot,
    clonotype,
    color_each = TRUE,
    default_color = "#808080",
    scale_bg = 1,
    fill_legend = TRUE
)

The function takes in a plot apotc_ggplot generated by APOTCPlot()/vizAPOTC() and modifies its underlying ggplot data to highlight/dim clones in clonotype. Read the function level docs for more information on how to customize the coloring of highlights with color_each and default_color.

A potentially useful application is to inspect the shared clonotypes:

# create the APackOfTheClones plot
apotc_plot <- pbmc %>%
    vizAPOTC(clonecall = "aa", show_labels = TRUE, verbose = FALSE)

# get the shared clonotypes
shared_clonotypes <- pbmc %>%
    getSharedClones(clonecall = "aa") %>%
    names()

# highlight the first 3 shared clones
apotc_plot %>%
    showCloneHighlight(shared_clonotypes[1:3])

APackOfTheClones documentation built on Oct. 11, 2024, 1:08 a.m.