cytof_heatmap {cytofkit} | R Documentation

## Heatmap plot of cluster mean value results

### Description

Heatmap plot of cluster mean value results

### Usage

    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))

### Arguments

`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.

### Value

A heatmap object from `gplots`

### Examples

    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")])

[Package cytofkit version 1.12.0 Index]