hallmarks {glmSparseNet} | R Documentation |
Retrieve hallmarks of cancer count for genes
hallmarks( genes, metric = "count", hierarchy = "full", generate.plot = TRUE, show.message = FALSE )
genes |
gene names |
metric |
see below |
hierarchy |
see below |
generate.plot |
flag to indicate if return object has a ggplot2 object |
show.message |
flag to indicate if run.cache method shows messages |
data.frame with choosen metric and hierarchy It also returns a vector with genes that do not have any hallmarks.
See http://chat.lionproject.net/api for more details on the metric and hallmarks parameters
To standardize the colors in the gradient you can use scale_fill_gradientn(limits=c(0,1), colours=topo.colors(3)) to limit between 0 and 1 for cprob and -1 and 1 for npmi
## Not run: hallmarks(c('MOB1A', 'RFLNB', 'SPIC')) hallmarks(c('MOB1A', 'RFLNB', 'SPIC'), metric = 'cprob') ## End(Not run)