plot_best_call {clustifyr} | R Documentation |
Plot best calls for each cluster on a tSNE or umap
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, ... )
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 |
ggplot object, cells projected by dr, colored by cell type classification
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" )