computeHeatmap {singleCellTK} | R Documentation

## computeHeatmap The computeHeatmap method computes the heatmap visualization for a set of features against a set of dimensionality reduction components. This method uses the heatmap computation algorithm code from `Seurat` but plots the heatmap using `ComplexHeatmap` and `cowplot` libraries.

### Description

computeHeatmap The computeHeatmap method computes the heatmap visualization for a set of features against a set of dimensionality reduction components. This method uses the heatmap computation algorithm code from `Seurat` but plots the heatmap using `ComplexHeatmap` and `cowplot` libraries.

### Usage

    computeHeatmap(
      inSCE,
      useAssay,
      dims = 10,
      nfeatures = 30,
      cells = NULL,
      reduction = "pca",
      disp.min = -2.5,
      disp.max = 2.5,
      balanced = TRUE,
      nCol = NULL,
      externalReduction = NULL
    )

### Arguments

`inSCE` | Input `SingleCellExperiment` object.
`useAssay` | The assay to use for heatmap computation.
`dims` | Specify the number of dimensions to use for heatmap. Default `10`.
`nfeatures` | Specify the number of features to use for heatmap. Default is `30`.
`cells` | Specify the samples/cells to use for heatmap computation. Default is `NULL` which will utilize all samples in the assay.
`reduction` | Specify the reduction slot in the input object. Default is `"pca"`.
`disp.min` | Specify the minimum dispersion value to use for floor clipping of assay values. Default is `-2.5`.
`disp.max` | Specify the maximum dispersion value to use for ceiling clipping of assay values. Default is `2.5`.
`balanced` | Specify if the number of of up-regulated and down-regulated features should be balanced. Default is `TRUE`.
`nCol` | Specify the number of columns in the output plot. Default is `NULL` which will auto-compute the number of columns.
`externalReduction` | Specify an external reduction if not present in the input object. This external reduction should be created using `CreateDimReducObject` function.

### Value

Heatmap plot object.

[Package singleCellTK version 2.2.0 Index]