Prefixed all the functions with gsa. in order to distinguish the methods from other possible methods of the same name in the namespace.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4738 348d0f76-0448-11de-a6fe-93d51630548a

R/src/gsalib/R/gsa.getargs.R

@@ -1,4 +1,4 @@
-.getargs.usage <- function(argspec, doc) {
+.gsa.getargs.usage <- function(argspec, doc) {
     cargs = commandArgs();
 
     usage = "Usage:";
@@ -34,7 +34,7 @@
     stop(call. = FALSE);
 }
 
-getargs <- function(argspec, doc = NA) {
+gsa.getargs <- function(argspec, doc = NA) {
     argsenv = new.env();
 
     for (argname in names(argspec)) {
@@ -66,7 +66,7 @@ getargs <- function(argspec, doc = NA) {
         cargs = commandArgs(TRUE);
 
         if (length(cargs) == 0) {
-            .getargs.usage(argspec, doc);
+            .gsa.getargs.usage(argspec, doc);
         }
 
         for (i in 1:length(cargs)) {
@@ -75,7 +75,7 @@ getargs <- function(argspec, doc = NA) {
                 value = cargs[i+1];
 
                 if (key == "h" | key == "help") {
-                    .getargs.usage(argspec, doc);
+                    .gsa.getargs.usage(argspec, doc);
                 }
 
                 if (length(grep("^[\\d\\.e\\+\\-]+$", value, perl=TRUE, ignore.case=TRUE)) > 0) {

R/src/gsalib/R/gsa.plot.venn.R

@@ -1,11 +1,9 @@
-plot.venn <-
+gsa.plot.venn <-
 function(a, b, c=0, a_and_b, a_and_c=0, b_and_c=0,
                      col=c("#FF6342", "#63C6DE", "#ADDE63"),
                      pos=c(0.20, 0.20, 0.80, 0.82),
                      debug=0
                     ) {
-    print("This is the gsalib plot.venn function");    
-
     library(png);
     library(graphics);
 

R/src/gsalib/R/gsa.read.eval.R

@@ -1,4 +1,4 @@
-.attemptToLoadFile <- function(filename) {
+.gsa.attemptToLoadFile <- function(filename) {
     file = NA;
 
     if (file.exists(filename) & file.info(filename)$size > 500) {
@@ -8,7 +8,7 @@
     file;
 }
 
-read.eval <-
+gsa.read.eval <-
 function(evalRoot) {
     fileAlleleCountStats = paste(evalRoot, ".AlleleCountStats.csv", sep="");
     fileCompOverlap = paste(evalRoot, ".Comp_Overlap.csv", sep="");
@@ -46,20 +46,20 @@ function(evalRoot) {
         CallsetFilteredNames = c()
     );
 
-    eval$AlleleCountStats                = .attemptToLoadFile(fileAlleleCountStats);
+    eval$AlleleCountStats                = .gsa.attemptToLoadFile(fileAlleleCountStats);
-    eval$CompOverlap                     = .attemptToLoadFile(fileCompOverlap);
+    eval$CompOverlap                     = .gsa.attemptToLoadFile(fileCompOverlap);
-    eval$CountVariants                   = .attemptToLoadFile(fileCountVariants);
+    eval$CountVariants                   = .gsa.attemptToLoadFile(fileCountVariants);
-    eval$GenotypeConcordance             = .attemptToLoadFile(fileGenotypeConcordance);
+    eval$GenotypeConcordance             = .gsa.attemptToLoadFile(fileGenotypeConcordance);
-    eval$MetricsByAc                     = .attemptToLoadFile(fileMetricsByAc);
+    eval$MetricsByAc                     = .gsa.attemptToLoadFile(fileMetricsByAc);
-    eval$MetricsBySample                 = .attemptToLoadFile(fileMetricsBySample);
+    eval$MetricsBySample                 = .gsa.attemptToLoadFile(fileMetricsBySample);
-    eval$Quality_Metrics_by_allele_count = .attemptToLoadFile(fileQuality_Metrics_by_allele_count);
+    eval$Quality_Metrics_by_allele_count = .gsa.attemptToLoadFile(fileQuality_Metrics_by_allele_count);
-    eval$QualityScoreHistogram           = .attemptToLoadFile(fileQualityScoreHistogram);
+    eval$QualityScoreHistogram           = .gsa.attemptToLoadFile(fileQualityScoreHistogram);
-    eval$SampleStatistics                = .attemptToLoadFile(fileSampleStatistics);
+    eval$SampleStatistics                = .gsa.attemptToLoadFile(fileSampleStatistics);
-    eval$SampleSummaryStatistics         = .attemptToLoadFile(fileSampleSummaryStatistics);
+    eval$SampleSummaryStatistics         = .gsa.attemptToLoadFile(fileSampleSummaryStatistics);
-    eval$SimpleMetricsBySample           = .attemptToLoadFile(fileSimpleMetricsBySample);
+    eval$SimpleMetricsBySample           = .gsa.attemptToLoadFile(fileSimpleMetricsBySample);
-    eval$TiTv                            = .attemptToLoadFile(fileTi_slash_Tv_Variant_Evaluator);
+    eval$TiTv                            = .gsa.attemptToLoadFile(fileTi_slash_Tv_Variant_Evaluator);
-    eval$TiTvStats                       = .attemptToLoadFile(fileTiTvStats);
+    eval$TiTvStats                       = .gsa.attemptToLoadFile(fileTiTvStats);
-    eval$Variant_Quality_Score           = .attemptToLoadFile(fileVariant_Quality_Score);
+    eval$Variant_Quality_Score           = .gsa.attemptToLoadFile(fileVariant_Quality_Score);
 
     uniqueJexlExpressions = unique(eval$TiTv$jexl_expression);
     eval$CallsetOnlyNames = as.vector(uniqueJexlExpressions[grep("FilteredIn|Intersection|none", uniqueJexlExpressions, invert=TRUE, ignore.case=TRUE)]);
@@ -69,6 +69,15 @@ function(evalRoot) {
         paste(gsub("^(\\w)", "In\\U\\1", eval$CallsetNames[2], perl=TRUE), "-Filtered", gsub("^(\\w)", "In\\U\\1", eval$CallsetNames[1], perl=TRUE), sep=""))
     );
 
+    if (!(eval$CallsetFilteredNames[1] %in% unique(eval$TiTv$jexl_expression))) {
+        eval$CallsetFilteredNames[1] = paste("In", eval$CallsetNames[1], "-FilteredIn", eval$CallsetNames[2], sep="");
+    }
+
+    if (!(eval$CallsetFilteredNames[2] %in% unique(eval$TiTv$jexl_expression))) {
+        eval$CallsetFilteredNames[2] = paste("In", eval$CallsetNames[2], "-FilteredIn", eval$CallsetNames[1], sep="");
+        #eval$CallsetFilteredNames[2] = paste(gsub("^(\\w)", "In", eval$CallsetNames[2], perl=TRUE), "-Filtered", gsub("^(\\w)", "In", eval$CallsetNames[1], perl=TRUE), sep="");
+    }
+
     eval;
 }
 

R/src/gsalib/R/gsa.read.gatkreport.R

@@ -1,5 +1,5 @@
 # Load a table into the specified environment.  Make sure that each new table gets a unique name (this allows one to cat a bunch of tables with the same name together and load them into R without each table overwriting the last.
-.assignGATKTableToEnvironment <- function(tableName, tableHeader, tableRows, tableEnv) {
+.gsa.assignGATKTableToEnvironment <- function(tableName, tableHeader, tableRows, tableEnv) {
     d = data.frame(tableRows, row.names=NULL, stringsAsFactors=FALSE);
     colnames(d) = tableHeader;
 
@@ -21,7 +21,7 @@
 }
 
 # Load all GATKReport tables from a file
-read.gatkreport <- function(filename) {
+gsa.read.gatkreport <- function(filename) {
     con = file(filename, "r", blocking = TRUE);
     lines = readLines(con);
     close(con);
@@ -57,7 +57,7 @@ read.gatkreport <- function(filename) {
     }
 
     if (!is.na(tableName)) {
-        .assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
+        .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
     }
 
     gatkreport = as.list(tableEnv);

R/src/gsalib/R/gsa.read.squidmetrics.R

@@ -1,4 +1,4 @@
-read.squidmetrics = function(project, bylane = FALSE) {
+gsa.read.squidmetrics = function(project, bylane = FALSE) {
     suppressMessages(library(ROracle));
 
     drv = dbDriver("Oracle");

R/src/gsalib/man/gsa.getargs.Rd

@@ -1,5 +1,5 @@
-\name{getargs}
+\name{gsa.getargs}
-\alias{getargs}
+\alias{gsa.getargs}
 \title{
 Get script arguments
 }
@@ -7,7 +7,7 @@ Get script arguments
 Get script arguments given a list object specifying arguments and documentation.  Can be used in command-line or interactive mode.  This is helpful when developing scripts in interactive mode that will eventually become command-line programs.  If no arguments are specified or help is requested in command-line mode, the script will print out a usage statement with available arguments and exit.
 }
 \usage{
-getargs(argspec, doc = NA)
+gsa.getargs(argspec, doc = NA)
 }
 \arguments{
   \item{argspec}{
@@ -18,7 +18,7 @@ A list object.  Each key is an argument name.  The value is another list object
 );
 }
 
-If the value provided is NA, the argument is considered required and must be specified when the script is invoked.  For command-line mode, this means the argument must be specified on the command-line.  In interactive mode, there are two ways of specifying these arguments.  First, if a properly formatted list argument called 'cmdargs' is present in the current environment (i.e. the object returned by getargs() from a previous invocation), the value is taken from this object.  Otherwise, the argument is prompted for.
+If the value provided is NA, the argument is considered required and must be specified when the script is invoked.  For command-line mode, this means the argument must be specified on the command-line.  In interactive mode, there are two ways of specifying these arguments.  First, if a properly formatted list argument called 'cmdargs' is present in the current environment (i.e. the object returned by gsa.getargs() from a previous invocation), the value is taken from this object.  Otherwise, the argument is prompted for.
 }
 
   \item{doc}{
@@ -50,7 +50,7 @@ argspec = list(
     test2   = list(value=2.3e9,          doc="Another argument that does stuff")
 );
         
-cmdargs = getargs(argspec, doc="My test program");
+cmdargs = gsa.getargs(argspec, doc="My test program");
 
 print(cmdargs$file);  # will print '[1] "/my/test.vcf"'
 }

R/src/gsalib/man/gsa.plot.venn.Rd

@@ -1,5 +1,5 @@
-\name{plot.venn}
+\name{gsa.plot.venn}
-\alias{plot.venn}
+\alias{gsa.plot.venn}
 \title{
 Plot a proportional venn diagram
 }
@@ -7,7 +7,7 @@ Plot a proportional venn diagram
 Plot a proportional venn diagram (two or three-way venns allowed)
 }
 \usage{
-plot.venn(a, b, c = 0, a_and_b, a_and_c = 0, b_and_c = 0, col = c("#FF6342", "#63C6DE", "#ADDE63"), pos = c(0.2, 0.2, 0.8, 0.82), debug = 0)
+gsa.plot.venn(a, b, c = 0, a_and_b, a_and_c = 0, b_and_c = 0, col = c("#FF6342", "#63C6DE", "#ADDE63"), pos = c(0.2, 0.2, 0.8, 0.82), debug = 0)
 }
 \arguments{
   \item{a}{
@@ -64,10 +64,10 @@ Kiran Garimella
 }
 \examples{
 ## Plot a two-way Venn diagram
-plot.venn(1000, 750, 0, 400);
+gsa.plot.venn(1000, 750, 0, 400);
 
 ## Plot a three-way Venn diagram
-plot.venn(1000, 750, 900, 400, 650, 500);
+gsa.plot.venn(1000, 750, 900, 400, 650, 500);
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.

R/src/gsalib/man/gsa.read.eval.Rd

@@ -1,5 +1,5 @@
-\name{read.eval}
+\name{gsa.read.eval}
-\alias{read.eval}
+\alias{gsa.read.eval}
 \title{
 Read a VariantEval file
 }
@@ -7,7 +7,7 @@ Read a VariantEval file
 Read a VariantEval file that's output in R format.
 }
 \usage{
-read.eval(evalRoot)
+gsa.read.eval(evalRoot)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

R/src/gsalib/man/gsa.read.gatkreport.Rd

@@ -1,13 +1,13 @@
-\name{read.gatkreport}
+\name{gsa.read.gatkreport}
-\alias{read.gatkreport}
+\alias{gsa.read.gatkreport}
 \title{
-read.gatkreport
+gsa.read.gatkreport
 }
 \description{
 Reads a GATKReport file - a multi-table document - and loads each table as a separate data.frame object in a list.
 }
 \usage{
-read.gatkreport(filename)
+gsa.read.gatkreport(filename)
 }
 \arguments{
   \item{filename}{
@@ -50,6 +50,6 @@ Kiran Garimella
 %% ~~objects to See Also as \code{\link{help}}, ~~~
 }
 \examples{
-report = read.gatkreport("/path/to/my/output.gatkreport");
+report = gsa.read.gatkreport("/path/to/my/output.gatkreport");
 }
 \keyword{ ~kwd1 }

R/src/gsalib/man/gsa.read.squidmetrics.Rd

@@ -1,13 +1,13 @@
-\name{read.squidmetrics}
+\name{gsa.read.squidmetrics}
-\alias{read.squidmetrics}
+\alias{gsa.read.squidmetrics}
 \title{
-read.squidmetrics
+gsa.read.squidmetrics
 }
 \description{
 Reads metrics for a specified SQUID project into a dataframe.
 }
 \usage{
-read.squidmetrics("C315")
+gsa.read.squidmetrics("C315")
 }
 \arguments{
   \item{project}{
@@ -43,6 +43,6 @@ This method will only work within the Broad Institute internal network.
 }
 \examples{
 ## Obtain metrics for project C315.
-d = read.squidmetrics("C315");
+d = gsa.read.squidmetrics("C315");
 }
 \keyword{ ~kwd1 }

R/src/gsalib/man/gsalib-package.Rd

@@ -25,7 +25,7 @@ GATK help forum: http://www.getsatisfaction.com/gsa
 }
 \examples{
 ## get script arguments in interactive and non-interactive mode
-cmdargs = getargs( list(
+cmdargs = gsa.getargs( list(
     requiredArg1 = list(
         value = NA,
         doc   = "Documentation for requiredArg1"
@@ -38,10 +38,10 @@ cmdargs = getargs( list(
 ) );
 
 ## plot a proportional Venn diagram
-plot.venn(500, 250, 0, 100);
+gsa.plot.venn(500, 250, 0, 100);
 
 ## read a GATKReport file
-report = gatk.report("/path/to/my/output.gatkreport");
+report = gsa.gatk.report("/path/to/my/output.gatkreport");
 
 ## emit a message
 gsa.message("This is a message");
@@ -51,5 +51,18 @@ gsa.message("This is a warning message");
 
 ## emit an error message
 gsa.message("This is an error message");
+
+## read the SQUID metrics for a given sequencing project (internal to the Broad only)
+s = gsa.read.squidmetrics("C427");
+
+## read command-line arguments
+cmdargs = gsa.getargs(
+    list(
+        file    = list(value="/my/test.vcf", doc="VCF file"),
+        verbose = list(value=0,              doc="If 1, set verbose mode"),
+        test2   = list(value=2.3e9,          doc="Another argument that does stuff")
+    ),
+    doc="My test program"
+);
 }
 \keyword{ package }