plotExprHeatmap {CATALYST} | R Documentation

## Plot expression heatmap

### Description

Heatmap of marker expressions aggregated by sample, cluster, or both; with options to include annotation of cell metadata factors, clustering(s), as well as relative and absolute cell counts.

### Usage

    plotExprHeatmap(
      x,
      features = NULL,
      by = c("sample_id", "cluster_id", "both"),
      k = "meta20",
      m = NULL,
      assay = "exprs",
      fun = c("median", "mean", "sum"),
      scale = c("first", "last", "never"),
      q = 0.01,
      row_anno = TRUE,
      col_anno = TRUE,
      row_clust = TRUE,
      col_clust = TRUE,
      row_dend = TRUE,
      col_dend = TRUE,
      bars = FALSE,
      perc = FALSE,
      bin_anno = FALSE,
      hm_pal = rev(brewer.pal(11, "RdYlBu")),
      k_pal = CATALYST:::.cluster_cols,
      m_pal = k_pal,
      distance = c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"),
      linkage = c("average", "ward.D", "single", "complete", "mcquitty", "median",
        "centroid", "ward.D2")
    )

### Arguments

`x` | a `SingleCellExperiment`.
`features` | character string specifying which features to include; valid values are `"type"/"state"` for `type/state_markers(x)` if `rowData(x)$marker_class` have been specified; a subset of `rownames(x)`; NULL to use all features. When `by = "both"`, only 1 feature is allowed.
`by` | character string specifying whether to aggregate by sample, cluster, both.
`k` | character string specifying which clustering to use when `by != "sample_id"`; `assay` data will be aggregated across these cluster IDs.
`m` | character string specifying a metaclustering to include as an annotation when `by != "sample_id"` and `row_anno = TRUE`.
`assay` | character string specifying which assay data to use; valid values are `assayNames(x)`.
`fun` | character string specifying the function to use as summary statistic.
`scale` | character string specifying the scaling strategy: `"first"`: scale & trim then aggregate `"last"`: aggregate then scale & trim `"never"`: aggregate only If `scale != "never"`, data will be scaled using lower (`q`%) and upper (`1-q`%) quantiles as boundaries.
`q` | single numeric in [0,0.5) determining the quantiles to trim when `scale != "never"`.
`row_anno, col_anno` | logical specifying whether to include row/column annotations (see details); when one axis corresponds to samples (`by != "cluster_id"`), this can be a character vector specifying a subset of `names(colData(x))` to be included as annotations.
`row_clust, col_clust` | logical specifying whether rows/columns should be hierarchically clustered and re-ordered accordingly.
`row_dend, col_dend` | logical specifying whether to include the row/column dendrograms.
`bars` | logical specifying whether to include a barplot of cell counts per cluster as a right-hand side row annotation.
`perc` | logical specifying whether to display percentage labels next to bars when `bars = TRUE`.
`bin_anno` | logical specifying whether to display values inside bins.
`hm_pal` | character vector of colors to interpolate for the heatmap.
`k_pal, m_pal` | character vector of colors to interpolate for cluster annotations when `by != "sample_id"`.
`distance` | character string specifying the distance metric to use for both row and column hierarchical clustering; passed to `Heatmap`
`linkage` | character string specifying the agglomeration method to use for both row and column hierarchical clustering; passed to `Heatmap`

### Details

By default (`row/col_anno = TRUE`), for axes corresponding to samples (y-axis for `by = "sample_id"` and x-axis for `by = "both"`), annotations will be drawn for all non-numeric cell metadata variables. Alternatively, a specific subset of annotations can be included for only a subset of variables by specifying `row/col_anno` to be a character vector in `names(colData(x))` (see examples).

For axes corresponding to clusters (y-axis for `by = "cluster_id"` and `"both"`), annotations will be drawn for the specified clustering(s) (arguments `k` and `m`).

### Value

a `Heatmap-class` object.

### Author(s)

Helena L Crowell helena.crowell@uzh.ch

### References

Nowicka M, Krieg C, Crowell HL, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

### See Also

`plotMedExprs`, `plotFreqHeatmap`, `plotMultiHeatmap`

### Examples

    data(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- cluster(sce)

    # median scaled & trimmed expression by cluster
    plotExprHeatmap(sce,
      by = "cluster_id", k = "meta8",
      scale = "first", q = 0.05, bars = FALSE)

    # scale each marker between 0 and 1
    # after aggregation (without trimming)
    plotExprHeatmap(sce,
      scale = "last", q = 0,
      bars = TRUE, perc = TRUE,
      hm_pal = hcl.colors(10, "YlGnBu", rev = TRUE))

    # raw (un-scaled) median expression by cluster-sample
    plotExprHeatmap(sce,
      features = "pp38", by = "both", k = "meta10",
      scale = "never", row_anno = FALSE, bars = FALSE)

    # include only subset of samples
    sub <- filterSCE(sce,
      patient_id != "Patient",
      sample_id != "Ref3")

    # includes specific annotations &
    # split into CDx & all other markers
    is_cd <- grepl("CD", rownames(sce))
    plotExprHeatmap(sub,
      rownames(sce)[is_cd],
      row_anno = "condition",
      bars = FALSE)
    plotExprHeatmap(sub,
      rownames(sce)[!is_cd],
      row_anno = "patient_id",
      bars = FALSE)

[Package CATALYST version 1.16.2 Index]