In jspaezp/sctree: Tree based analysis of single rna-seq clusters

Returning Garnett Classifiers

We provide an interface to export the decision trees as garnett classifiers for more information on the specification please visit: https://cole-trapnell-lab.github.io/garnett/docs/#submitting-a-classifier

library(sctree)
data("small_5050_mix")
DimPlot(small_5050_mix)

tree_fit <- fit_ctree(small_5050_mix, cluster = "0", minprob = 0.1, alpha = 0.01)
plot(tree_fit)

plot_flowstyle(small_5050_mix, c("ASNS", "ADA", "TSC22D3"))

as.garnett(tree_fit)

Exporting the garnett classifier to a file

tmp <- as.garnett(tree_fit)
class(tmp)

tmp2 <- print(tmp)
class(tmp2)

jspaezp/sctree documentation built on April 30, 2020, 10:36 p.m.