plot_gene_pairs: Plot paired usage of V(D)J segments across chains

In rnabioco/AVIDtools: A collection of single-cell V(D)J tools

Plot paired usage of V(D)J segments across chains

Description

Plot the paired usage of V(D)J segments across two chains. For example, plot_gene_pairs() can be used to plot the frequency that different TRA and TRB V segments appear together.

Usage

plot_gene_pairs(
  input,
  data_col,
  chains,
  cluster_col = NULL,
  genes = 20,
  chain_col = global$chain_col,
  method = "heatmap",
  units = "percent",
  return_list = FALSE,
  sep = global$sep,
  plot_colors = NULL,
  plot_lvls = NULL,
  trans = "identity",
  rotate_labels = FALSE,
  panel_nrow = NULL,
  ...
)

Arguments

input	Object containing V(D)J data. If a data.frame is provided, the cell barcodes should be stored as row names.
data_col	meta.data column containing V(D)J genes identified for each clonotype.
chains	Chains to use for calculating usage of different gene pairs. This should be a character vector containing the two chains to use for calculations, e.g. c("IGH", "IGK").
cluster_col	meta.data column containing cell clusters to use when calculating gene usage
genes	An integer specifying the number of genes to plot, or a vector giving the names of genes to include.
chain_col	meta.data column containing chains for each cell
method	Method to use for plotting, possible values are: 'heatmap', create a heatmap, this is the default when two columns are passed to the data_cols argument 'circos', create a circos plot, this requires two columns to be provided to the data_cols argument
units	Units to show on scale, either 'frequency' or 'percent'
return_list	Should a list of plots be returned, if FALSE plots will be combined and arranged into panels
sep	Separator used for storing per-chain V(D)J data for each cell
plot_colors	Character vector containing colors to use for plot. If a bar graph is created this will specify how to color cell clusters. For a heatmap, these colors will be used to generate the color gradient.
plot_lvls	Levels to use for ordering clusters
trans	Transformation to use when plotting segment usage, e.g. 'log10'. By default values are not transformed, refer to ggplot2::continuous_scale() for more options.
rotate_labels	Should labels on circos plot be rotated to reduce overlapping text
panel_nrow	The number of rows to use for arranging plots when return_list is FALSE
...	Additional arguments to pass to plotting function, ggplot2::geom_tile() for heatmap, circlize::chordDiagram() for circos plot

Value

ggplot object

See Also

calc_gene_pairs(), calc_gene_usage(), plot_gene_usage()

Examples

# Plot the frequency of different V genes for IGH and IGK chains
plot_gene_pairs(
  vdj_sce,
  data_col    = "v_gene",
  chains      = c("IGH", "IGK"),
  cluster_col = "orig.ident"
)

rnabioco/AVIDtools documentation built on Oct. 28, 2023, 10:23 a.m.