Create MDS plot

Calculate MDS coordinates based on a beta diversity metric and plot results.

Usage

plot_mds(
  input,
  data_col,
  cluster_col,
  method = "jaccard",
  chain = NULL,
  chain_col = global$chain_col,
  plot_colors = NULL,
  plot_lvls = names(plot_colors),
  label_points = TRUE,
  n_label = "none",
  label_params = list(),
  sep = global$sep,
  ...
)

Arguments

input

Single cell object or data.frame 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 values to use for calculating pairwise similarity between clusters, e.g. 'clonotype_id'

cluster_col

meta.data column containing cluster IDs to use for calculating overlap

method

Method to use for comparing clusters and calculating MDS coordinates, available methods include:

• 'jaccard', Jaccard dissimilarity index implemented with abdiv::jaccard()

• 'horn_morisita', Horn-Morisita index implemented with abdiv::horn_morisita()

chain

Chain to use for comparing clusters. To perform calculations using a single chain, the column passed to data_col must contain per-chain data such as CDR3 sequences. Set to NULL to include all chains.

chain_col

meta.data column containing chains for each cell

plot_colors

Character vector containing colors for plotting

plot_lvls

Levels to use for ordering clusters

label_points

Label points on plot

n_label

Location on plot where n label should be added, this can be any combination of the following:

• 'corner', display the total number of points plotted in the top right corner, the position of the label can be modified by passing x and y specifications with the label_params argument

• 'none', do not display the number of points plotted

label_params

Named list providing additional parameters to modify n label aesthetics, e.g. list(size = 4, color = "red")

sep

Separator used for storing per-chain V(D)J data for each cell

...

Additional arguments to pass to ggplot2::geom_point()

Value

ggplot object

See also

calc_mds(), calc_similarity(), plot_similarity(), MASS::isoMDS()

Examples

# Calculate MDS coordinates
plot_mds(
  vdj_sce,
  data_col = "clonotype_id",
  cluster_col = "isotype"
)


# Calculate MDS coordinates based on IGK CDR3 sequences
plot_mds(
  vdj_sce,
  data_col    = "cdr3",
  cluster_col = "isotype",
  chain       = "IGK"
)


# Calculate repertoire similarity using the Horn-Morisita index
plot_mds(
  vdj_sce,
  data_col    = "clonotype_id",
  cluster_col = "isotype",
  method      = "horn_morisita"
)