hallmarks: Retrieve hallmarks of cancer count for genes

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

Retrieve hallmarks of cancer count for genes

Description

The API has been removed and this function is no longer available.

Usage

hallmarks(
  genes,
  metric = "count",
  hierarchy = "full",
  generate.plot = TRUE,
  show.message = FALSE
)

Arguments

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

Value

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

sysbiomed/glmSparseNet documentation built on Feb. 17, 2024, 1:38 p.m.