cytof_heatmap: Heatmap plot of cluster mean value results
In raman91/cytofkit2: cytofkit: an integrated mass cytometry data analysis pipeline

Description Usage Arguments Value Examples

Heatmap plot of cluster mean value results

cytof_heatmap(data, baseName = "Cluster", scaleMethod = "none",
  dendrogram = c("both", "row", "column", "none"),
  colPalette = c("bluered", "greenred", "spectral1", "spectral2"),
  cex_row_label = NULL, cex_col_label = NULL, key.par = list(mgp =
  c(1.5, 0.5, 0), mar = c(3, 2.5, 3.5, 1)), keysize = 1.4,
  margins = c(5, 5))

`data`	A matrix with rownames and colnames
`baseName`	The name as a prefix in the title of the heatmap.
`scaleMethod`	Method indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is 'none'.
`dendrogram`	Control the dengrogram on row or column, selection includes 'both', 'row', 'column', 'none'.
`colPalette`	Use selected colour palette, includes 'bluered', 'greenred', 'spectral1' and 'spectral2'.
`cex_row_label`	Text size for row labels.
`cex_col_label`	Text size for column labels.
`key.par`	Graphical parameters for the color key.
`keysize`	Numeric value indicating the size of the key.
`margins`	Numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively.

A heatmap object from gplots

m1 <- c(rnorm(300, 10, 2), rnorm(400, 4, 2), rnorm(300, 7))
m2 <- c(rnorm(300, 4), rnorm(400, 16), rnorm(300, 10, 3))
m3 <- c(rnorm(300, 16), rnorm(400, 40, 3), rnorm(300, 10))
m4 <- c(rnorm(300, 7, 3), rnorm(400, 30, 2), rnorm(300, 10))
m5 <- c(rnorm(300, 27), rnorm(400, 40, 1),rnorm(300, 10))
c <- c(rep(1,300), rep(2,400), rep(3,300))
rnames <- paste(paste('sample_', c('A','B','C','D'), sep = ''), 
rep(1:250,each = 4), sep='_') 
exprs_cluster <- data.frame(cluster = c, m1 = m1, m2 = m2, m3 = m3, m4 = m4, m5 = m5)
row.names(exprs_cluster) <- sample(rnames, 1000)
cluster_mean <- aggregate(. ~ cluster, data = exprs_cluster, mean)
rownames(cluster_mean) <- paste("cluster_", cluster_mean$cluster, sep = "")
cytof_heatmap(cluster_mean[, -which(colnames(cluster_mean) == "cluster")])