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Integrate (optional) progress bar - as a replacement for cat('.') #3

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418d482
Integrate (optional) progress bar (https://github.com/kvnkuang/pbmcap…
krassowski Jan 18, 2018
d2fd137
Document newly added progress_bar parameter
krassowski Jan 18, 2018
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23 changes: 18 additions & 5 deletions R/ActiveDriver.R
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ assess_all_regions = function(active_site_regions, mut_pos, active_site_pos, dis
}


create_gene_record = function(gene, fasta, mut, pho, disorder, flank=7, mid_flank=2, simplified=FALSE, all_sites_together=FALSE, skip_mismatch=TRUE, type="poisson", enriched_only=TRUE) {
create_gene_record = function(gene, fasta, mut, pho, disorder, flank=7, mid_flank=2, simplified=FALSE, all_sites_together=FALSE, skip_mismatch=TRUE, type="poisson", enriched_only=TRUE, show_progress=TRUE) {
l = list()
l$gene = gene
l$protein_sequence = fasta[[gene]]
Expand Down Expand Up @@ -218,7 +218,9 @@ create_gene_record = function(gene, fasta, mut, pho, disorder, flank=7, mid_flan
l$mutations_input$active_region = l$active_regions[l$mutations_input$position]
}
}
cat(".")
if (show_progress) {
cat(".")
}
gc()
l
}
Expand Down Expand Up @@ -301,6 +303,8 @@ check_mutations_and_sites = function(seqs_to_check, muts_to_check, sites_to_chec
#' @param enriched_only true/false to indicate whether only sites with enriched active site mutations will be included
#' in the final p-value estimation (TRUE is default). If FALSE, sites with less than expected mutations will be also
#' included.
#' @param progress_bar true/false to indicate whether a progress bar should be displayed. Default value is FALSE.
#' Requires pbmcapply.
#'
#' @return list with the following components:
#' @return all_active_mutations - table with mutations that hit or flank an active site. Additional columns of
Expand All @@ -327,7 +331,7 @@ check_mutations_and_sites = function(seqs_to_check, muts_to_check, sites_to_chec
#' kin_results = ActiveDriver(sequences, sequence_disorder, mutations, kinase_domains, simplified=TRUE)
#' @export

ActiveDriver = function(sequences, seq_disorder, mutations, active_sites, flank = 7, mid_flank = 2, mc.cores = 1, simplified = FALSE, return_records = FALSE, skip_mismatch = TRUE, regression_type = "poisson", enriched_only = TRUE) {
ActiveDriver = function(sequences, seq_disorder, mutations, active_sites, flank = 7, mid_flank = 2, mc.cores = 1, simplified = FALSE, return_records = FALSE, skip_mismatch = TRUE, regression_type = "poisson", enriched_only = TRUE, progress_bar = FALSE) {

# first initiate mutation counts if needed
if(is.null(mutations$count)) {mutations$count=1}
Expand Down Expand Up @@ -359,9 +363,18 @@ ActiveDriver = function(sequences, seq_disorder, mutations, active_sites, flank
}

cat("genes:", length(genes_to_test))
gene_records = parallel::mclapply(genes_to_test, create_gene_record,

if(progress_bar) {
mclapply = pbmcapply::pbmclapply
}
else {
mclapply = parallel::mclapply
}

gene_records = mclapply(genes_to_test, create_gene_record,
sequences, mutations, active_sites, seq_disorder, flank=flank, mid_flank=mid_flank,
mc.cores=mc.cores, simplified=simplified, skip_mismatch=skip_mismatch, type=regression_type, enriched_only=enriched_only, mc.preschedule=F)
mc.cores=mc.cores, simplified=simplified, skip_mismatch=skip_mismatch, type=regression_type,
enriched_only=enriched_only, mc.preschedule=F, show_progress=!progress_bar)
names(gene_records) = sapply(gene_records, '[[', 'gene')

all_gene_based_fdr = do.call("rbind",
Expand Down