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nice pheatmap

Source: R/visualization.R
pHeatmap.Rd

create and save a nice pheatmap in the folder heatmap using color breaks

Usage

pHeatmap(
  matrix,
  scale = "none",
  height = ceiling(nrow(matrix)/3),
  width = ceiling(ncol(matrix)/2),
  cellwidth = 10,
  cellheight = 10,
  treeheight_row = 10,
  treeheight_col = 10,
  fontsize = 10,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  annotation_row = NA,
  dir_output = "."
)

Arguments

matrix

numeric matrix of the values to be plotted

scale

should the values be centered and scaled in row, column direction? Allowed: row, column, none (default: none)

height

height of output plot (default: number of rows divided by three)

width

width of output plot (default: number of columns divided by two)

cellwidth

individual cell width (default: 10)

cellheight

individual cell height (default: 10)

treeheight_row

height of a tree for rows (default: 10)

treeheight_col

height of a tree for columns (default: 10)

fontsize

fontsize (default: 10)

cluster_rows

cluster rows? (default: true)

cluster_cols

cluster columns? (default: true)

annotation_row

data frame that contains the annotations. Rows in the data and in the annotation are matched using row names. (default: NA)

dir_output

directory to save the output plot (default: ".")

Value

save heatmap to folder

Examples

matrix <- matrix(rnorm(100), nrow = 10, ncol = 10)
rownames(matrix) <- paste0("Gene", 1:10)
colnames(matrix) <- paste0("Sample", 1:10)
pHeatmap(matrix, scale = "row", dir_output = ".")

#> pdf 
#>   2 
unlink("hm_matrix.pdf")