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 1.0.3 Index]