plot_best_call: Plot best calls for each cluster on a tSNE or umap

In NCBI-Hackathons/clustifyR: Classifier for Single-cell RNA-seq Using Cell Clusters

Plot best calls for each cluster on a tSNE or umap

Description

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"
)

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

NCBI-Hackathons/clustifyR documentation built on Aug. 31, 2024, 5:35 a.m.