Plot heatmap of cluster/factor correspondence
Generates matrix of cluster/factor correspondence, using sum of row-normalized factor loadings for every cell in each cluster. Plots heatmap of matrix, with red representing high total loadings for a factor, black low. Optionally can also include dendrograms and sorting for factors and clusters.
plotClusterFactors( object, use.aligned = FALSE, Rowv = NA, Colv = "Rowv", col = NULL, return.data = FALSE, ... )
object |
|
use.aligned |
Use quantile normalized factor loadings to generate matrix (default FALSE). |
Rowv |
Determines if and how the row dendrogram should be computed and reordered. Either a dendrogram or a vector of values used to reorder the row dendrogram or NA to suppress any row dendrogram (and reordering) (default NA for no dendrogram). |
Colv |
Determines if and how the column dendrogram should be reordered. Has the same options as the Rowv argument (default 'Rowv' to match Rowv). |
col |
Color map to use (defaults to red and black) |
return.data |
Return matrix of total factor loadings for each cluster (default FALSE). |
... |
Additional parameters to pass on to heatmap() |
If requested, matrix of size num_cluster x num_factor
## Not run: # ligerex (liger object), factorization complete input # plot expression for CD4 and return plots loading.matrix <- plotClusterFactors(ligerex, return.data = TRUE) ## End(Not run)
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