showCloneHighlight {APackOfTheClones}

Highlight specific clones on an APackOfTheClones ggplot

Description

This is an analogue for scRepertoire::highlightClones that can highlight certain clonotypes on an APackOfTheClones clonal expansion plot. For most combinations of the arguments, there will be a ggplot fill legend on the right side that correspond to each (existing) clonotype.

Usage

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

Arguments

apotc_ggplot

A ggplot object that is the output of APOTCPlot or vizAPOTC of an APackOfTheClones plot to be highlighted on.

clonotype

character vector of the sequence(s) to highlight. Note that it must be of the clonecall of the code that created the plot. A warning will be shown if any of the sequences are not present.

color_each

Either a logical of length 1, or a character(s). It is TRUE by default, which assigns a unique default ggplot color to each highlighted clone. If FALSE, each highlighted clone will retain its current color and no legend based on color is shown. A possible application here is to simply gauge the distribution of any shared clone. It can also indicate the uniform color of each highlighted clone: if it is a character of length 1, all highlighted clones will be of that color. Else it must be a character vector of the same length as clonotype, with each color corresponding to the clone. Here is a suitable place to use any palette function from the many other CRAN palette packages such as "viridis" or "RColorBrewer". Note that currently, the user must ensure clonotype contains only unique characters.

default_color

A character of length 1 or NULL indicating the color of non-highlighted clones. If NULL, all un-highlighted sequences will retain their original color in sc.data. Else, if it is a character, it should be a valid color that all un-highlighted clones are. Defaults to the hexcode for gray.

scale_bg

A positive numeric. Scales the brightness value of each color of the non-highlighted clones by itself as a scaling factor. Defaults to 1 which will not alter the current brightness. Note that if color_each = FALSE and default_color = NULL, this is equivalent to not highlighting any clones - in this case, it may be useful to alter scale_bg slightly so that the non-highlighted clones are darkened/brightened.

fill_legend

logical indicating whether a ggplot legend of the "fill" of each clonotype should be displayed.

Details

Under the hood, this function simply mutates the plotting dataframe under ⁠$data⁠ in the ggplot object, and operates on a column named color.

Note that if color_each = FALSE and default_color = NULL, this is equivalent to simply not highlighting anything and a warning will be shown.

Value

A ggplot object with the data modified to the highlighted colors

Examples

library(magrittr)
data("combined_pbmc")

# piping the plot can be nice to read syntatically -
# By default, assigns unique colors to highlights and everything else is gray
vizAPOTC(combined_pbmc, clonecall = "aa", verbose = FALSE) %>%
    showCloneHighlight("CASLSGSARQLTF_CASSSTVAGEQYF")

# one useful application is to highlight shared clones - beware that the
# clonotype sequences may get extremely long in the legend
shared_aa_clones <- names(getSharedClones(combined_pbmc, clonecall = "aa"))
vizAPOTC(combined_pbmc, clonecall = "aa", verbose = FALSE) %>%
    showCloneHighlight(shared_aa_clones)