plot_best_call {clustifyr} | R Documentation

## 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"
    )

[Package clustifyr version 1.4.0 Index]