plotHeatmap: Visualization heatmap of data of CYT

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

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	A 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)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.