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inferelator.R no longer needs to be run from the directory where it l… #1

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19 changes: 17 additions & 2 deletions R_scripts/summarize_results.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,20 @@
library('Matrix')
source('R_scripts/evaluate.R')

thisFile <- function() {
cmdArgs <- commandArgs(trailingOnly = FALSE)
needle <- "--file="
match <- grep(needle, cmdArgs)
if (length(match) > 0) {
# Rscript
return(normalizePath(sub(needle, "", cmdArgs[match])))
} else {
# 'source'd via R console
return(normalizePath(sys.frames()[[1]]$ofile))
}
}
baseDirectory <- dirname(thisFile())

source(paste(sep="/",baseDirectory,'R_scripts/evaluate.R'))

get.mean.and.lh <- function(mat) {
ret <- list()
Expand Down Expand Up @@ -62,7 +77,7 @@ sum.net <- function(betas, betas.resc, comb.confs, IN, cc.file, th=0.5) {
cat('A total of', length(gp$pred.has.na), 'predictors contained NA and were removed.\n')
cat('A total of', length(gp$pred.is.const), 'predictors were constant and were removed.\n')
cat('A total of', length(unique(unlist(gp$pred.groups))), 'predictors formed', length(gp$pred.groups), 'groups.\n')
source('R_scripts/evaluate.R')
source(paste(sep="/",baseDirectory,'R_scripts/evaluate.R'))
cc.aupr <- aupr(comb.confs, p.mat, eval.on.subset=TRUE)
cat('AUPR is', cc.aupr, '\n')

Expand Down
18 changes: 17 additions & 1 deletion R_scripts/vis_res_tfa.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,21 @@
library('Matrix')
source('R_scripts/priors.R')

# Get the directory in which inferelator.R sits
thisFile <- function() {
cmdArgs <- commandArgs(trailingOnly = FALSE)
needle <- "--file="
match <- grep(needle, cmdArgs)
if (length(match) > 0) {
# Rscript
return(normalizePath(sub(needle, "", cmdArgs[match])))
} else {
# 'source'd via R console
return(normalizePath(sys.frames()[[1]]$ofile))
}
}
baseDirectory <- dirname(thisFile())

source(paste(sep="/",baseDirectory,'R_scripts/priors.R'))

ChristophsPR <- function(ord.idx, gs) {
prec <- cumsum(gs[ord.idx]) / cumsum(rep(1, length(ord.idx)))
Expand Down
39 changes: 27 additions & 12 deletions inferelator.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,17 +10,32 @@ library('Matrix')
rm(list=ls())
gc()

source('R_scripts/utils.R')
source('R_scripts/design_and_response.R')
source('R_scripts/priors.R')
source('R_scripts/mi_and_clr.R')
source('R_scripts/bayesianRegression.R')
source('R_scripts/men.R')
source('R_scripts/evaluate.R')
source('R_scripts/tfa.R')
source('R_scripts/group_predictors.R')
source('R_scripts/summarize_results.R')
source('R_scripts/vis_tfs_and_targets.R')
# Get the directory in which inferelator.R sits
thisFile <- function() {
cmdArgs <- commandArgs(trailingOnly = FALSE)
needle <- "--file="
match <- grep(needle, cmdArgs)
if (length(match) > 0) {
# Rscript
return(normalizePath(sub(needle, "", cmdArgs[match])))
} else {
# 'source'd via R console
return(normalizePath(sys.frames()[[1]]$ofile))
}
}
baseDirectory <- dirname(thisFile())

source(paste(sep="/", baseDirectory, 'R_scripts/utils.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/design_and_response.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/priors.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/mi_and_clr.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/bayesianRegression.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/men.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/evaluate.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/tfa.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/group_predictors.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/summarize_results.R'))
source(paste(sep="/", baseDirectory, 'R_scripts/vis_tfs_and_targets.R'))


date.time.str <- format(Sys.time(), "%Y-%m-%d_%H-%M-%S")
Expand Down Expand Up @@ -429,7 +444,7 @@ PROCTIME <- proc.time() - start.proc.time
save(PARS, IN, SEED, PROCTIME, file = paste(PARS$save.to.dir, "/params_and_input.RData", sep=""))

# generate network report and visualize TFs and targets
source('R_scripts/net_report_new.R')
source(paste(sep="/", baseDirectory, 'R_scripts/net_report_new.R'))
Sys.sleep(2)
for (ccf in list.files(PARS$save.to.dir, pattern='combinedconf_*', full.names=TRUE)) {
if (PARS$output.report) {
Expand Down