plotHeatmap {CytoTree} | R Documentation

## Visualization heatmap of data of CYT

### Description

Visualization heatmap of data of CYT

### Usage

    plotHeatmap(
      object,
      markers = NULL,
      color = colorRampPalette(c("blue", "white", "red"))(100),
      scale = "row",
      downsize = 1000,
      cluster_rows = FALSE,
      cluster_cols = FALSE,
      ...
    )

### Arguments

`object` | An CYT object
`markers` | vector. markers to plot on the heatmap
`color` | vector. Colors used in heatmap.
`scale` | character. Whether the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"
`downsize` | numeric. Cells size used to plot heatmap
`cluster_rows` | logical. Whether rows should be clustered
`cluster_cols` | logical. Whether columns should be clustered
`...` | options to pass on to the `pheatmap` function.

### Value

ggplot2 figure

### Examples

    cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
    cyt <- readRDS(file = cyt.file)

    plotHeatmap(cyt)
    plotHeatmap(cyt, cluster_rows = TRUE)
    plotHeatmap(cyt, cluster_rows = TRUE, clustering_method = "ward.D")
    plotHeatmap(cyt, cluster_rows = TRUE, cluster_cols = TRUE)

[Package CytoTree version 1.4.0 Index]