plot_similarity: Plot repertoire similarity

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

Plot repertoire similarity

Description

Plot repertoire similarity

Usage

plot_similarity(
  input,
  data_col,
  cluster_col,
  group_col = NULL,
  method = abdiv::jaccard,
  chain = NULL,
  chain_col = global$chain_col,
  cluster_heatmap = TRUE,
  sep = global$sep,
  plot_colors = NULL,
  plot_lvls = names(plot_colors),
  rotate_labels = FALSE,
  remove_upper_triangle = FALSE,
  remove_diagonal = remove_upper_triangle,
  ...
)

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
group_col	meta.data column to use for grouping cluster IDs present in cluster_col. This is useful when there are multiple replicates or patients for each treatment condition.
method	Method to use for comparing clusters, possible values are: A function that takes two numeric vectors containing counts for each clonotype in the object, such as most beta diversity functions provided by the abdiv package. This will generate a heatmap. 'count', count the number of clonotypes overlapping between each cluster, this will generate a heatmap. 'circos', create a circos plot summarizing the overlap between clusters
chain	Chain to use for comparing clusters. To perform calculations using a single chain, the column passed to the data_col argument 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
cluster_heatmap	If FALSE, rows and columns of heatmap will not be clustered.
sep	Separator used for storing per-chain V(D)J data for each cell
plot_colors	Character vector containing colors for plotting
plot_lvls	Levels to use for ordering clusters
rotate_labels	Should labels on circos plot be rotated to reduce overlapping text
remove_upper_triangle	If TRUE, upper triangle for heatmap will not be shown.
remove_diagonal	If TRUE, diagonal for heatmap will not be shown.
...	Additional arguments to pass to plotting function, ComplexHeatmap::Heatmap() for heatmap, circlize::chordDiagram() for circos plot

Value

heatmap or circos plot

See Also

calc_similarity(), calc_mds(), plot_mds()

Examples

# Plot repertoire overlap
# use clonotype IDs present in 'clonotype_id' column for calculations
plot_similarity(
  vdj_sce,
  data_col    = "clonotype_id",
  cluster_col = "orig.ident"
)

# Specify method to use for calculating repertoire overlap
plot_similarity(
  vdj_sce,
  data_col    = "clonotype_id",
  cluster_col = "orig.ident",
  method      = abdiv::morisita
)

# Specify colors to use for heatmap
plot_similarity(
  vdj_sce,
  data_col    = "clonotype_id",
  cluster_col = "orig.ident",
  plot_color  = c("white", "red")
)

# Create circos plot
plot_similarity(
  vdj_sce,
  data_col    = "clonotype_id",
  cluster_col = "orig.ident",
  method      = "circos"
)

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