Dendrogram Behavior (Rowv, Colv)

• If either Rowv or Colv are already dendrograms, they are honored and their ordering is preserved (not reordered).
• Otherwise, dendrograms are computed as \(dd \leftarrow \text{as.dendrogram}(\text{hclustfun}(\text{distfun}(X)))\), where \(X\) is either \(x\) or \(t(x)\).
• If either is a vector (of “weights”), the appropriate dendrogram (\(dd\)) is reordered according to the supplied values, subject to the constraints imposed by the dendrogram, using \(\texttt{reorder}(dd, Rowv)\) (in the row case).
• If either is missing (as by default), the ordering of the corresponding dendrogram is by the mean value of the rows/columns (e.g., \(Rowv \leftarrow \text{rowMeans}(x, \text{na.rm=na.rm})\) in the row case).
• If either is NULL, no reordering will be done for the corresponding side.

Data Scaling (scale)

• If scale="row" (or scale="col"), the rows (columns) are scaled to have mean zero and standard deviation one.
• This scaling has some empirical evidence of being useful in genomic plotting.

Color Selection

• The default colors range from red to white (\(\texttt{heat.colors}\)) and are generally not considered aesthetically pleasing.
• Consider using enhancements like the RColorBrewer package to select better colors.

Plot Layout (Default and Customization)

• By default, four components are displayed in the plot:
  • Top left: The color key.
  • Top right: The column dendrogram.
  • Bottom left: The row dendrogram.
  • Bottom right: The image plot (heatmap).
• When RowSideColor or ColSideColor are provided, an additional row or column is inserted in the appropriate location.
• This layout can be overridden by specifying appropriate values for lmat, lwid, and lhei:
  • lmat controls the relative position of each element.
  • lwid controls the column width.
  • lhei controls the row height.
• See the help page for layout for details on how to use these arguments.

Note

• The original rows and columns are reordered to match the dendrograms Rowv and Colv (if present).
• heatmap.2() uses layout to arrange the plot elements. Consequentially, it cannot be used in a multi-column/row layout using layout(...), par(mfrow=...) or (mfcol=...).

demonstrate the effect of row and column dendrogram options

heatmap.2(x)                    ## default - dendrogram plotted and reordering done.

heatmap.2(x, dendrogram="none") ##  no dendrogram plotted, but reordering done.

heatmap.2(x, dendrogram="row")  ## row dendrogram plotted and row reordering done.

heatmap.2(x, dendrogram="col")  ## col dendrogram plotted and col reordering done.

heatmap.2(x, keysize=2)         ## default - dendrogram plotted and reordering done.

heatmap.2(x, Rowv=FALSE, dendrogram="both") ## generates a warning!

heatmap.2(x, Rowv=NULL, dendrogram="both")  ## generates a warning!
heatmap.2(x, Colv=FALSE, dendrogram="both") ## generates a warning!

Reorder dendrogram by branch means rather than sums

heatmap.2(x, reorderfun=function(d, w) reorder(d, w, agglo.FUN = mean) )

Color dendrograms’ branches (using dendextend)

full <- heatmap.2(x) # we use it to easily get the dendrograms

library(dendextend)  # for color_branches
heatmap.2(x, 
        Rowv=color_branches(full$rowDendrogram, k = 3),
        Colv=color_branches(full$colDendrogram, k = 2))

# Look at the vignette for more details:
# https://cran.r-project.org/web/packages/dendextend/vignettes/dendextend.html

plot a sub-cluster using the same color coding as for the full heatmap

full <- heatmap.2(x)

heatmap.2(x, Colv=full$colDendrogram[[2]], breaks=full$breaks)  # column subset

heatmap.2(x, Rowv=full$rowDendrogram[[1]], breaks=full$breaks)  # row subset

heatmap.2(x, Colv=full$colDendrogram[[2]],
            Rowv=full$rowDendrogram[[1]], breaks=full$breaks)  # both