simpleheatmap3: heatmap3 facade

In protViz/quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

Description

heatmap3 facade

Usage

simpleheatmap3(pln, main = "", distf = dist, hclustf = hclust,
  labRow = "", labCol = "", palette = getBlueWhiteRed(),
  margins = c(5, 5), scale = "none", plot = TRUE,
  nrOfClustersCol = 3, nrOfClustersRow = 3,
  suppressColSideCols = FALSE, ColSideLabs = "", RowSideLabs = "",
  ...)

Arguments

pln	matrix or dataframe with numerical values
main	title
distf	distance function
hclustf	clustering function
labRow	row labels
labCol	column labels
palette	color palette
margins	control margins of heatmap
scale	c(row, column or none)
plot	logical; If TRUE simpleheatmap3 returns modified heatmap3 object, if FALSE returns a data.frame with clusterIDs. Default is TRUE
nrOfClustersCol	number of distinct clusters for cutree function on columns. Default is 3
nrOfClustersRow	number of distinct clusters for cutree function on rows. Default is 3
suppressColSideCols	Option to suppress color side labelling per default
ColSideLabs	label for ColSideColors
RowSideLabs	label for RowSideColors
...	other parameters to heatmap3

Examples

df <- matrix(rnorm(150), ncol = 10) # 15x10 matrix without NAs

clust <- simpleheatmap3(pln = df,
                        main = "",
                        distf = dist,
                        hclustf = hclust,
                        labRow = "",
                        plot = FALSE,
                        nrOfClustersRow = 3,
                        suppressColSideCols = TRUE) 
# plot = F will return a list containing two data.frames 
# with the specified number of distinct clusters in nrOfClustersRow
# and nrOfClustersCol
clust
hmp3 <- simpleheatmap3(pln = df,
                       main = "",
                       distf = dist,
                       hclustf = hclust,
                       labRow = "",
                       plot = TRUE,
                       nrOfClustersRow = 3, 
                       nrOfClustersCol = 3, 
                       suppressColSideCols = FALSE)
# plot = TRUE will result in the same list and additionally plot the heatmap. 
# suppressColSideCols = FALSE will leave the heatmap with ColSideColors

stopifnot(all(clust$Row$clusterID==hmp3$Row$clusterID))

df[3,1:7] <- NA # Seed some missing values in line 3

hmp3_withNAs <- simpleheatmap3(pln = df,
                       main = "",
                       distf = dist,
                       hclustf = hclust,
                       labRow = paste0("ABC", 1:nrow(df)),
                       plot = TRUE,
                       nrOfClustersRow = 3, 
                       nrOfClustersCol = 3, 
                       suppressColSideCols = TRUE)
                       
# Since line 3 contained more than ncol(df)/2 missing values 
# it is removed from the clustering.

stopifnot(! 3 %in% hmp3_withNAs$Row$rowID)
hmp3_withNAs <- simpleheatmap3(pln = df,
                       main = "",
                       distf = dist,
                       hclustf = hclust,
                       labRow = paste0("ABC", 1:nrow(df)),
                       plot = TRUE,
                       nrOfClustersRow = 3, 
                       nrOfClustersCol = 3, 
                       suppressColSideCols = FALSE)
                       

protViz/quantable documentation built on Nov. 29, 2021, 10:07 a.m.