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 1.2.0 Index]