b09810165e57a61fc8e61549ea87da8b2dca3f58 kent Mon Jan 11 15:50:41 2021 -0800 Changing some Barchart to BarChart that I'd missed. diff --git src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c index 4f32403..bdaeb3a 100644 --- src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c +++ src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c @@ -1,39 +1,39 @@ -/* clusterMatrixToBarchartBed - Compute a barchart bed file from a gene matrix +/* clusterMatrixToBarChartBed - Compute a barchart bed file from a gene matrix * and a gene bed file and a way to cluster samples. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "localmem.h" #include "obscure.h" #include "sqlNum.h" boolean clSimple = FALSE; boolean clMedian = FALSE; char *clName2 = NULL; void usage() /* Explain usage and exit. */ { errAbort( - "clusterMatrixToBarchartBed - Compute a barchart bed file from a gene matrix\n" + "clusterMatrixToBarChartBed - Compute a barchart bed file from a gene matrix\n" "and a gene bed file and a way to cluster samples.\n" "NOTE: consider using matrixClusterColumns and matrixToBarChartBed instead\n" "usage:\n" - " clusterMatrixToBarchartBed sampleClusters.tsv geneMatrix.tsv geneset.bed output.bed\n" + " clusterMatrixToBarChartBed sampleClusters.tsv geneMatrix.tsv geneset.bed output.bed\n" "where:\n" " sampleClusters.tsv is a two column tab separated file with sampleId and clusterId\n" " geneMatrix.tsv has a row for each gene. The first row uses the same sampleId as above\n" " geneset.bed has the maps the genes in the matrix (from it's first column) to the genome\n" " geneset.bed needs 6 standard bed fields. Unless name2 is set it also needs a name2\n" " field as the last field\n" " output.bed is the resulting bar chart, with one column per cluster\n" "options:\n" " -simple - don't store the position of gene in geneMatrix.tsv file in output\n" " -median - use median (instead of mean)\n" " -name2=twoColFile.tsv - get name2 from file where first col is same ase geneset.bed's name\n" ); } /* Command line validation table. */ @@ -57,39 +57,39 @@ /* Find cluster in cluster hash, if it doesn't exist make it. */ char *clusterName = row[1]; struct hashEl *hel = hashLookup(clusterHash, clusterName); if (hel == NULL) hel = hashAddInt(clusterHash, clusterName, 1); else hel->val = ((char *)hel->val)+1; // Increment hash pointer as per hashIncInt char *clusterStableName = hel->name; // This is allocated in clusterHash hashAdd(sampleHash, row[0], clusterStableName); } lineFileClose(&lf); *retSampleHash = sampleHash; *retClusterHash = clusterHash; } -void clusterMatrixToBarchartBed(char *sampleClusters, char *matrixTsv, char *geneBed, char *output) -/* clusterMatrixToBarchartBed - Compute a barchart bed file from a gene matrix +void clusterMatrixToBarChartBed(char *sampleClusters, char *matrixTsv, char *geneBed, char *output) +/* clusterMatrixToBarChartBed - Compute a barchart bed file from a gene matrix * and a gene bed file and a way to cluster samples. */ { /* Figure out if we need to do medians etc */ boolean doMedian = clMedian; /* Load up the gene set */ -verbose(2, "clusterMatrixToBarchartBed(%s,%s,%s,%s)\n", sampleClusters, matrixTsv, geneBed, output); +verbose(2, "clusterMatrixToBarChartBed(%s,%s,%s,%s)\n", sampleClusters, matrixTsv, geneBed, output); int bedRowSize = 0; struct hash *geneHash = hashTsvBy(geneBed, 3, &bedRowSize); verbose(2, "%d columns about %d genes in %s\n", bedRowSize, geneHash->elCount, geneBed); /* Deal with external gene hash */ struct hash *nameToName2 = NULL; if (clName2 != NULL) { int colCount = 0; nameToName2 = hashTsvBy(clName2, 0, &colCount); if (colCount != 2) errAbort("Expecting %s to be a two column tab separated file", clName2); } /* Keep track of how many fields gene bed has to have and locate name2 */ @@ -312,18 +312,18 @@ verbose(1, "matrix total %g, %d clusters, %g ave/cluster\n", sumTotal, clusterCount, sumTotal/clusterCount); } carefulClose(&f); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 5) usage(); clSimple = optionExists("simple"); clMedian = optionExists("median"); clName2 = optionVal("name2", clName2); -clusterMatrixToBarchartBed(argv[1], argv[2], argv[3], argv[4]); +clusterMatrixToBarChartBed(argv[1], argv[2], argv[3], argv[4]); return 0; }