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

Source: R/calc-gene-usage.R
plot_gene_pairs.Rd

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"
)