plotHeatmap {CytoTree} | R Documentation |
Visualization heatmap of data of CYT
plotHeatmap( object, markers = NULL, color = colorRampPalette(c("blue", "white", "red"))(100), scale = "row", downsize = 1000, cluster_rows = FALSE, cluster_cols = FALSE, ... )
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 |
ggplot2 figure
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)