Plot best calls for each cluster on a tSNE or umap — plot_best_call (original) (raw)

Plot best calls for each cluster on a tSNE or umap

Usage

plot_best_call(
  cor_mat,
  metadata,
  cluster_col = "cluster",
  collapse_to_cluster = FALSE,
  threshold = 0,
  x = "UMAP_1",
  y = "UMAP_2",
  plot_r = FALSE,
  per_cell = FALSE,
  ...
)

Arguments

cor_mat

input similarity matrix

metadata

input metadata with tsne or umap coordinates and cluster ids

cluster_col

metadata column, can be cluster or cellid

collapse_to_cluster

if a column name is provided, takes the most frequent call of entire cluster to color in plot

threshold

minimum correlation coefficent cutoff for calling clusters

x

x variable

y

y variable

plot_r

whether to include second plot of cor eff for best call

per_cell

whether the cor_mat was generate per cell or per cluster

...

passed to plot_dims

Value

ggplot object, cells projected by dr, colored by cell type classification

Examples

res <- clustify(
    input = pbmc_matrix_small,
    metadata = pbmc_meta,
    ref_mat = cbmc_ref,
    query_genes = pbmc_vargenes,
    cluster_col = "classified"
)
#> using # of genes: 599
#> similarity computation completed, matrix of 9 x 13, preparing output

plot_best_call(
    cor_mat = res,
    metadata = pbmc_meta,
    cluster_col = "classified"
)