VDJ_plot_SHM: Plotting of somatic hypermutation counts

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Plotting of somatic hypermutation counts

Description

Plots for SHM based on MIXCR output generated using the VDJ_call_MIXCR function and appended to the VDJ.GEX.matrix.output

Usage

VDJ_plot_SHM(
  VDJ.mixcr.matrix,
  group.by,
  quantile.label,
  point.size,
  mean.line.color,
  stats.to.console,
  platypus.version
)

Arguments

VDJ.mixcr.matrix	Output dataframe from the VDJ_call_MIXCR function or a dataframe generated using the VDJ_GEX_matrix function and supplemented with MIXCR information
group.by	Character. Defaults to "sample_id". Column name of VDJ.matrix to split VDJ.matrix by. For each unique entry in that column a set of plots will be generated. This can be useful to plot SHM by expansion or by transcriptomics-derived clusters
quantile.label	Numeric. Defaults to 0.9. Which points to label in the SHM scatterplot. If set to 0.9, the top 10% of cells by SHM number will be labelled. If ggrepel throws a warning, concerning overlap it is recommended to attempt to lable less points to avoid cluttering
point.size	Size of points in plots. Passed to geom_jitter()
mean.line.color	Color of mean bar in dotplots. Passed to geom_errorbar()
stats.to.console	Boolean. Defaults to FALSE. Prints basic statistics (AOV \+ post hoc test) to console
platypus.version	Character. Only "v3" available.

Value

Returns a list of ggplot objects. out\[\[1\]\] is a boxplot comparing SHM by group.by. out\[\[2\]\] to out\[\[n\]\] are plots for each group that visualize VDJ and VJ SHM distribution for each group. Data for any plot can be accessed via out \[\[any\]\]$data

Examples

small_vgm <- Platypus::small_vgm
small_vgm[[1]]$VDJ_SHM <- as.integer(rnorm(nrow(small_vgm[[1]]), mean = 5, sd = 3))
small_vgm[[1]]$VJ_SHM <- as.integer(rnorm(nrow(small_vgm[[1]]), mean = 5, sd = 3))

SHM_plots <- VDJ_plot_SHM(VDJ = small_vgm[[1]]
, group.by = "sample_id", quantile.label = 0.9)

SHM_plots <- VDJ_plot_SHM(VDJ = small_vgm[[1]]
, group.by = "seurat_clusters", quantile.label = 0.99)

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.