moduleHeatmap {celda} | R Documentation

## Heatmap for featureModules

### Description

Renders a heatmap for selected featureModules. Cells are ordered from those with the lowest probability of the module on the left to the highest probability on the right. If more than one module is used, then cells will be ordered by the probabilities of the first module only. Features are ordered from those with the highest probability in the module on the top to the lowest probability on the bottom.

### Usage

    moduleHeatmap(
      counts,
      celdaMod,
      featureModule = 1,
      topCells = 100,
      topFeatures = NULL,
      normalizedCounts = NA,
      scaleRow = scale,
      showFeaturenames = TRUE
    )

### Arguments

`counts` | Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celdaMod'.
`celdaMod` | Celda object of class 'celda_G' or 'celda_CG'.
`featureModule` | Integer Vector. The featureModule(s) to display. Multiple modules can be included in a vector.
`topCells` | Integer. Number of cells with the highest and lowest probabilities for this module to include in the heatmap. For example, if 'topCells' = 50, the 50 cells with the lowest probability and the 50 cells with the highest probability for that featureModule will be included. If NULL, all cells will be plotted. Default 100.
`topFeatures` | Integer. Plot 'topFeatures' with the highest probability in the featureModule. If NULL, plot all features in the module. Default NULL.
`normalizedCounts` | Integer matrix. Rows represent features and columns represent cells. This matrix should correspond to the one provided for 'counts', but should be passed through. If NA, normalize 'counts'. Default NA. 'normalizeCounts(counts, "proportion", transformationFun=sqrt)'. Use of this parameter is particularly useful for plotting many moduleHeatmaps, where normalizing the counts matrix repeatedly would be too time consuming.
`scaleRow` | Character. Which function to use to scale each individual row. Set to NULL to disable. Occurs after normalization and log transformation. For example, 'scale' will Z-score transform each row. Default 'scale'.
`showFeaturenames` | Logical. Wheter feature names should be displayed. Default TRUE.

### Value

A list containing row and column dendrograms as well as a gtable for grob plotting

### Examples

    data(celdaCGSim, celdaCGMod)
    moduleHeatmap(celdaCGSim$counts, celdaCGMod)

[Package celda version 1.2.4 Index]