pbHeatmap {muscat} | R Documentation

## Heatmap of cluster-sample pseudobulks

### Description

...

### Usage

    pbHeatmap(
      x,
      y,
      k = NULL,
      g = NULL,
      c = NULL,
      top_n = 20,
      fdr = 0.05,
      lfc = 1,
      sort_by = "p_adj.loc",
      decreasing = FALSE,
      assay = "logcounts",
      fun = mean,
      normalize = TRUE,
      col = viridis(10),
      row_anno = TRUE,
      col_anno = TRUE
    )

### Arguments

`x` | a `SingleCellExperiment`.
`y` | a list of DS analysis results as returned by `pbDS` or `mmDS`.
`k` | character vector; specifies which cluster ID(s) to retain. Defaults to `levels(x$cluster_id)`.
`g` | character vector; specifies which genes to retain. Defaults to considering all genes.
`c` | character string; specifies which contrast/coefficient to retain. Defaults to `names(y$table)[1]`.
`top_n` | single numeric; number of genes to retain per cluster.
`fdr, lfc` | single numeric; FDR and logFC cutoffs to filter results by. The specified FDR threshold is applied to `p_adj.loc` values.
`sort_by` | character string specifying a numeric results table column to sort by; `"none"` to retain original ordering.
`decreasing` | logical; whether to sort in decreasing order of `sort_by`.
`assay` | character string; specifies which assay to use; should be one of `assayNames(x)`.
`fun` | function to use as summary statistic, e.g., mean, median, sum (depending on the input assay).
`normalize` | logical; whether to apply a z-normalization to each row (gene) of the cluster-sample pseudobulk data.
`col` | character vector of colors or color mapping function generated with `colorRamp2`. Passed to argument `col` in `Heatmap` (see `?ComplexHeatmap::Heatmap` for details).
`row_anno, col_anno` | logical; whether to render annotations of cluster and group IDs, respectively.

### Value

a `HeatmapList-class` object.

### Author(s)

Helena L Crowell

### Examples

    data(sce)

    # compute pseudobulks & run DS analysis
    pb <- aggregateData(sce)
    res <- pbDS(pb)

    # cluster-sample expression means
    pbHeatmap(sce, res)

    # include only a single cluster
    pbHeatmap(sce, res, k = "B cells")

    # plot specific gene across all clusters
    pbHeatmap(sce, res, g = "ISG20")

[Package muscat version 1.2.1 Index]