view.aspects {scde} | R Documentation

## View heatmap

### Description

Internal function to visualize aspects of transcriptional heterogeneity as a heatmap. Used by `pagoda.view.aspects`.

### Usage

    view.aspects(mat, row.clustering = NA, cell.clustering = NA, zlim = c(-1,
      1) * quantile(mat, p = 0.95), row.cols = NULL, col.cols = NULL,
      cols = colorRampPalette(c("darkgreen", "white", "darkorange"), space =
      "Lab")(1024), show.row.var.colors = TRUE, top = Inf, ...)

### Arguments

`mat` | Numeric matrix
`row.clustering` | Row dendrogram
`cell.clustering` | Column dendrogram
`zlim` | Range of the normalized gene expression levels, inputted as a list: c(lower_bound, upper_bound). Values outside this range will be Winsorized. Useful for increasing the contrast of the heatmap visualizations. Default, set to the 5th and 95th percentiles.
`row.cols` | Matrix of row colors.
`col.cols` | Matrix of column colors. Useful for visualizing cell annotations such as batch labels.
`cols` | Heatmap colors
`show.row.var.colors` | Boolean of whether to show row variance as a color track
`top` | Restrict output to the top n aspects of heterogeneity
`...` | additional arguments for heatmap plotting

### Value

A heatmap

[Package scde version 2.12.0 Index]