## testing ##
library(devtools)
library(readr)
# setwd('~/Work/iAtlas/Subtypes/Subtype-Classifier/')
# using the package
#devtools::install_github("Gibbsdavidl/ImmuneSubtypeClassifier", force = T)
devtools::install_github("Gibbsdavidl/ImmuneSubtypeClassifier")
reload(pkgload::inst('ImmuneSubtypeClassifier'))
library(ImmuneSubtypeClassifier)
load('~/ebpp_signature_genes.rda')
#fitting all models
breakVec=c(0, 0.25, 0.5, 0.75, 1.0)
params=list(max_depth = 5, eta = 0.3, nrounds = 100, nthread = 5, nfold=5)
# list of models
ens <- fitEnsembleModel(Xmat, Y, n=10, sampSize=0.7, ptail=0.05, params=params, breakVec=breakVec)
save(ens, file='~/ensemble_model.rda')
# calling subtypes on the test set
calls <- callEnsemble(ens, Xmat)
# model performance plots
perfs <- subtypePerf(calls, Y)
library(gridExtra)
x <- grid.arrange(perfs[[1]]$plot,perfs[[2]]$plot,perfs[[3]]$plot,perfs[[4]]$plot,perfs[[5]]$plot,perfs[[6]]$plot, ncol=6, nrow=1 )
save(ens, file='~/ensemble_model_signatures_genes.rda')
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