feature_map: Plot heatmap of basis matrix

In ccfindR: Cancer Clone Finder

Description

Generate heatmap of features derived from factorization of count data.

Usage

feature_map(object, basis.matrix = NULL, rank, markers = NULL,
  subtract.mean = TRUE, log = TRUE, max.per.cluster = 10,
  feature.names = NULL, perm = NULL, main = "Feature map",
  cscale = NULL, cex.cluster = 1, cex.feature = 0.5, mar = NULL,
  ...)

Arguments

object	Object of class scNMFSet.
basis.matrix	Basis matrix can be supplied instead of object.
rank	Rank value for which the gene map is to be displayed. The object must contain the corresponding slot (one element of basis(object)[[k]] for which ranks(object)[[k]]==rank.
markers	Vector of gene names containing markers to be included in addition to the metagenes. All entries of rowData(object) matching them will be added to the metagene list.
subtract.mean	Process each rows of basis matrix W by standardization using the mean of elements within the row.
log	If TRUE, subtract.mean uses geometric mean and division. Otherwise, use arithmetic mean and subtraction.
max.per.cluster	Maximum number of metagenes per cluster.
feature.names	Names to be used in the plot for features.
perm	Permutation of cluster IDs.
main	Main title.
cscale	Colors for heatmap.
cex.cluster	Cluster ID label size.
cex.feature	Feature ID label size.
mar	Margins for graphics::par.
...	Other arguments to be passed to image, and plot.

Details

This function uses image() and is more flexible than gene_map.

If object contains multiple ranks, only the requested rank's basis matrix W will be displayed. As in gene_map, the features displayed in rows are selected by "max" scheme

Value

NULL

Examples

 
set.seed(1)
x <- simulate_data(nfeatures=10,nsamples=c(20,20,60))
rownames(x) <- seq_len(10)
 
set.seed(1)
x <- simulate_data(nfeatures=10,nsamples=c(20,20,60))
rownames(x) <- seq_len(10)
colnames(x) <- seq_len(100)
s <- scNMFSet(count=x,rowData=seq_len(10), colData=seq_len(100))
s <- vb_factorize(s,ranks=seq(2,5))
plot(s)
feature_map(s, rank=3)

ccfindR documentation built on Nov. 8, 2020, 5:12 p.m.