plot_mds: Create MDS plot

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

Create MDS plot

Description

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"
)

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