overcluster_test {clustifyr} | R Documentation

## compare clustering parameters and classification outcomes

### Description

compare clustering parameters and classification outcomes

### Usage

    overcluster_test(
      expr,
      metadata,
      ref_mat,
      cluster_col,
      x_col = "UMAP_1",
      y_col = "UMAP_2",
      n = 5,
      ngenes = NULL,
      query_genes = NULL,
      threshold = 0,
      do_label = TRUE,
      do_legend = FALSE,
      newclustering = NULL,
      combine = TRUE
    )

### Arguments

`expr` | expression matrix
`metadata` | metadata including cluster info and dimension reduction plotting
`ref_mat` | reference matrix
`cluster_col` | column of clustering from metadata
`x_col` | column of metadata for x axis plotting
`y_col` | column of metadata for y axis plotting
`n` | expand n-fold for over/under clustering
`ngenes` | number of genes to use for feature selection, use all genes if NULL
`query_genes` | vector, otherwise genes with be recalculated
`threshold` | type calling threshold
`do_label` | whether to label each cluster at median center
`do_legend` | whether to draw legend
`newclustering` | use kmeans if NULL on dr or col name for second column of clustering
`combine` | if TRUE return a single plot with combined panels, if FALSE return list of plots (default: TRUE)

### Value

faceted ggplot object

### Examples

    set.seed(42)
    overcluster_test(
        expr = pbmc_matrix_small,
        metadata = pbmc_meta,
        ref_mat = cbmc_ref,
        cluster_col = "classified",
        x_col = "UMAP_1",
        y_col = "UMAP_2"
    )

[Package clustifyr version 1.6.0 Index]