diff --git a/R/ADPRpages.R b/R/ADPRpages.R index 4c7664a89..755ceaf6c 100644 --- a/R/ADPRpages.R +++ b/R/ADPRpages.R @@ -8,7 +8,7 @@ library(ReadImages) ##defaults<-par(no.readonly = TRUE) -tearsheet<-function(lanetable, sampletable, variant, pulldesc){ +tearsheet<-function(lanetable, sampletable, variant, Protocol, Sequencer){ #define layout layout(matrix(c(1,1,2,4,3,5), ncol=2, nrow=3, byrow=TRUE), heights=c(1, 2.5,2.5,), respect=FALSE) @@ -54,7 +54,8 @@ tearsheet<-function(lanetable, sampletable, variant, pulldesc){ #Calc by sample metrics attach(bysample); - + baits<-Bait.Set[1] + alllanes<-signif(sum(X..Lanes.included.in.aggregation, na.rm = TRUE)) mean.lanes.samp<-signif(mean(X..Lanes.included.in.aggregation, na.rm = TRUE)); sd.lanes.samp<-signif(sd(X..Lanes.included.in.aggregation, na.rm=TRUE)); mean.mrl.samp<-signif(mean(Mean.Read.Length, na.rm=TRUE)); @@ -81,8 +82,8 @@ tearsheet<-function(lanetable, sampletable, variant, pulldesc){ detach(variant) #prep stuff. - summary<-c(nrow(bysample), pulldesc[1], pulldesc[2], paste(callable.target, "bases")) - summary2<-c(pulldesc[3], pulldesc[4], paste(mean.lanes.samp, "+/-", sd.lanes.samp), paste(singlelanes, "single lanes,", pairedlanes, "paired lanes"), paste(mean.mrl.samp, "+/-", sd.mrl.samp)) + summary<-c(nrow(bysample), Protocol, baits, paste(callable.target, "bases")) + summary2<-c(Sequencer, alllanes, paste(mean.lanes.samp, "+/-", sd.lanes.samp), paste(singlelanes, "single lanes,", pairedlanes, "paired lanes"), paste(mean.mrl.samp, "+/-", sd.mrl.samp)) samps<-paste(meansamp, c("M", "M", "x", "%", "%", "%"), " +/- ", sdsamp, c("M", "M", "x", "%", "%", "%"), sep="") lanes<-paste(meanlane, c("M", "M", "x", "%", "%", "%"), " +/- ", sdlane, c("M", "M", "x", "%", "%", "%"), sep="") @@ -277,7 +278,7 @@ titvsamp<-function(metricsbysamp){ } -functionalclasses<-function(countfunctclasses){} +#functionalclasses<-function(countfunctclasses){} errorratepercycle<-function(erpc){ @@ -411,13 +412,16 @@ depth_sample<-function(DOC2){ datapuller<-function(setname){ #library(yaml) - lanes<-read.delim(paste(setname, "lanes.txt", sep=""), header=TRUE) - samps<-read.delim(paste(setname, "samps.txt", sep=""), header=TRUE) - doct<-read.delim(paste(setname, "depth.sample_interval_summary", sep=""), header=TRUE, row.names=1) - docs<-read.delim(paste(setname, ".depth.sample_summary", sep=""), header=TRUE, row.names=1) - eval<-read.csv(paste(setname, "", sep="")) - titv<-read.csv(paste(setname, ".eval.SimpleMetricsBySample.csv", sep=""), skip=1) - erprp<-read.delim(paste(setname, ".erprp", sep="")) + strsplit(setname, ".")[1]->projectname + + + lanes<-read.delim(paste(projectname, "_lanes.txt", sep=""), header=TRUE) + samps<-read.delim(paste(projectname, "_samps.txt", sep=""), header=TRUE) + #doct<-read.delim(paste(setname, "depth.sample_interval_summary", sep=""), header=TRUE, row.names=1) + #docs<-read.delim(paste(setname, ".depth.sample_summary", sep=""), header=TRUE, row.names=1) + #eval<-read.csv(paste(setname, "eval.CountFunctionalClasses", sep=""), skip=1) + titv<-read.csv(paste(setname, ".eval.SimpleMetricsBySample.csv", sep=""), skip=1) + #erprp<-read.delim(paste(setname, ".erprp", sep="")) colnames(lanes)<-c('Initiative','Project','GSSR.ID','External.ID','WR.ID','Flowcell','Lane','Lane.Type','Library','AL_TOTAL_READS','AL_PF_READS','AL_PCT_PF_READS','AL_PF_NOISE_READS','AL_PF_READS_ALIGNED','AL_PCT_PF_READS_ALIGNED','AL_PF_HQ_ALIGNED_READS','AL_PF_HQ_ALIGNED_BASES','AL_PF_HQ_ALIGNED_Q20_BASES','AL_PF_HQ_MEDIAN_MISMATCHES','AL_MEAN_READ_LENGTH','AL_READS_ALIGNED_IN_PAIRS','AL_PCT_READS_ALIGNED_IN_PAIRS','AL_BAD_CYCLES','AL_PCT_STRAND_BALANCE','DUP_UNPAIRED_READS_EXAMINED','DUP_READ_PAIRS_EXAMINED','DUP_UNMAPPED_READS','DUP_UNPAIRED_READ_DUPLICATES','DUP_READ_PAIR_DUPLICATES','DUP_PERCENT_DUPLICATION','DUP_ESTIMATED_LIBRARY_SIZE','HS_BAIT_SET','HS_GENOME_SIZE','HS_LIBRARY_SIZE','HS_BAIT_TERRITORY','HS_TARGET_TERRITORY','HS_BAIT_DESIGN_EFFICIENCY','HS_TOTAL_READS','HS_PF_READS','HS_PF_UNIQUE_READS','HS_PCT_PF_READS','HS_PCT_PF_UQ_READS','HS_PCT_PF_UQ_READS_ALIGNED','HS_PF_UQ_READS_ALIGNED','HS_PF_UQ_BASES_ALIGNED','HS_ON_BAIT_BASES','HS_NEAR_BAIT_BASES','HS_OFF_BAIT_BASES','HS_ON_TARGET_BASES','HS_PCT_SELECTED_BASES','HS_PCT_OFF_BAIT','HS_ON_BAIT_VS_SELECTED','HS_MEAN_BAIT_COVERAGE','HS_MEAN_TARGET_COVERAGE','HS_FOLD_ENRICHMENT','HS_ZERO_CVG_TARGETS_PCT','HS_FOLD_80_BASE_PENALTY','HS_PCT_TARGET_BASES_2X','HS_PCT_TARGET_BASES_10X','HS_PCT_TARGET_BASES_20X','HS_PCT_TARGET_BASES_30X','HS_PENALTY_10X','HS_PENALTY_20X','HS_PENALTY_30X','SNP_TOTAL_SNPS','SNP_PCT_DBSNP','SNP_NUM_IN_DBSNP','Lane.IC.Matches','Lane.IC.PCT.Mean.RD1.Err.Rate','Lane.IC.PCT.Mean.RD2.Err.Rate','FP_PANEL_NAME','FP_PANEL_SNPS','FP_CONFIDENT_CALLS','FP_CONFIDENT_MATCHING_SNPS','FP_CONFIDENT_CALLED_PCT','FP_CONFIDENT_MATCHING_SNPS_PCT','LPCNCRD_REFERENCE','LPCNCRD_NON_REFERENCE','LPCNCRD_PCT_CONCORDANCE') @@ -427,27 +431,30 @@ datapuller<-function(setname){ } -runner<-function(basename, desc){ +runner<-function(basename, desc1, desc2){ datapuller(basename)->tables attach(tables) - pdf("tester9-15.pdf", width=22, height=15,pointsize=24) + + + pdf(paste(basename, ".pdf", sep=""), width=22, height=15,pointsize=24) - tearsheet(lanes, samps, titv, pulldesc) + tearsheet(lanes, samps, titv, desc1, desc1) fingerprints(lanes) snps_called(lanes) titvsamp(titv) - functionalclasses(eval) - errorratepercycle(erprp) - depth_target(doct) - depth_sample(docs) + #functionalclasses(eval) + #errorratepercycle(erprp) + #depth_target(doct) + #depth_sample(docs) dev.off() detach(tables) } - - +if(length(commandArgs(TRUE))>0){ + runner(commandArgs(TRUE)) + }