9a51fe6723423851ee77535b465399a52e244084 kent Mon Jan 11 18:16:04 2021 -0800 Improving usage statement per code review #26745 diff --git src/utils/matrixToBarChartBed/matrixToBarChartBed.c src/utils/matrixToBarChartBed/matrixToBarChartBed.c index 32a0b73..dcc0b65 100644 --- src/utils/matrixToBarChartBed/matrixToBarChartBed.c +++ src/utils/matrixToBarChartBed/matrixToBarChartBed.c @@ -1,262 +1,265 @@ /* matrixToBarChartBed - Attach a labeled expression matrix to a bed file joining on the bed's * name column.. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "obscure.h" #include "rainbow.h" #include "sqlNum.h" int clBedIx = 4; void usage() /* Explain usage and exit. */ { errAbort( "matrixToBarChartBed - Attach a labeled expression matrix to a bed file joining\n" "on the matrix's first column and the bed's name column.\n" "usage:\n" " matrixToBarChartBed matrix.tsv mapping.bed barChartOutput.bed\n" "where\n" " matrix is tab-separated values with the first row and column used as labels\n" " mapping.bed maps a row of the matrix using the bed's name field and matrix's 1st field\n" + " The mapping.bed file is expected to have a 'name2' field as it's last column\n" + " and otherwise be at least bed 6. Only the first 6 fields plus the name2 field are\n" + " used. Often this file will be made with gencodeVersionForGenes\n" "options:\n" " -bedIx=N - use the N'th column of the mapping.bed as the id column. Default %d\n" " -trackDb=stanza.txt -output a trackDb stanza for this as a track\n" " -stats=stats.tsv - stats file from matrixClusterColumns, makes coloring in trackDb better\n" , clBedIx); } /* Command line validation table. */ static struct optionSpec options[] = { {"bedIx", OPTION_INT}, {"trackDb", OPTION_STRING}, {"stats", OPTION_STRING}, {NULL, 0}, }; struct matrixClusterStats /* Stats on a clustering of a matrix */ { struct matrixClusterStats *next; /* Next in singly linked list. */ char *cluster; /* The name of the cluster */ int count; /* The number of samples clustered together from old matrix */ double total; /* The sum of all samples */ }; struct matrixClusterStats *matrixClusterStatsLoad(char **row) /* Load a matrixClusterStats from row fetched with select * from matrixClusterStats * from database. Dispose of this with matrixClusterStatsFree(). */ { struct matrixClusterStats *ret; AllocVar(ret); ret->cluster = cloneString(row[0]); ret->count = sqlSigned(row[1]); ret->total = sqlDouble(row[2]); return ret; } struct matrixClusterStats *matrixClusterStatsLoadAllByChar(char *fileName, char chopper) /* Load all matrixClusterStats from a chopper separated file. * Dispose of this with matrixClusterStatsFreeList(). */ { struct matrixClusterStats *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = matrixClusterStatsLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } void writeBarChartTrack(char *fileName, char *statsFile, char *name, int sampleCount, char *sampleNames[]) /* Make a one-stanza trackDb file that describes our barchart */ { FILE *f = mustOpen(fileName, "w"); fprintf(f, "track %s\n", name); fprintf(f, "type bigBarChart\n"); fprintf(f, "visibility pack\n"); fprintf(f, "shortLabel %s\n", name); fprintf(f, "longLabel %s\n", name); fprintf(f, "barChartMetric unknown\n"); fprintf(f, "barChartUnit unknown\n"); fprintf(f, "defaultLabelFields name\n"); fprintf(f, "labelFields name,name2\n"); fprintf(f, "bigDataUrl %s.bb\n", name); /* Load optional stats into hash */ struct hash *statsHash = NULL; if (statsFile != NULL) { struct matrixClusterStats *el, *list = matrixClusterStatsLoadAllByChar(statsFile, '\t'); uglyf("Got %d items on list\n", slCount(list)); statsHash = hashNew(0); for (el = list; el != NULL; el = el->next) hashAdd(statsHash, el->cluster, el); } /* Print colors */ fprintf(f, "barChartColors"); double pos = 0.0; double step = 1.0/sampleCount; int i; for (i=0; i<sampleCount; ++i) { struct rgbColor color = saturatedRainbowAtPos(pos); if (statsHash == NULL) fprintf(f, " #%02x%02x%02x", color.r, color.g, color.b); else { double belief = 1.0; char *sample = sampleNames[i]; struct matrixClusterStats *stats = hashFindVal(statsHash, sample); if (stats == NULL) errAbort("%s is in matrixFile but not %s", sample, statsFile); if (stats->count < 50) belief *= 0.7; if (stats->count < 10) belief *= 0.7; if (stats->total < 1e6) belief *= 0.7; if (stats->total < 1e5) belief *= 0.7; double doubt = 1.0 - belief; int maxColor = 255; int r = color.r * belief + maxColor*doubt; int g = color.g * belief + maxColor*doubt; int b = color.b * belief + maxColor*doubt; fprintf(f, " #%02x%02x%02x", r, g, b); } pos += step; } fprintf(f, "\n"); /* print labels */ fprintf(f, "barChartBars"); for (i=0; i<sampleCount; ++i) { char *sample = cloneString(sampleNames[i]); subChar(sample, ' ', '_'); fprintf(f, " %s", sample); freeMem(sample); } fprintf(f, "\n"); carefulClose(&f); } void matrixToBarChartBed(char *matrixTsv, char *geneBed, char *statsFile, char *output, int bedIx, char *trackDb) /* matrixToBarChartBed - Attach a labeled expression matrix to a bed file joining on the bed's * name column.. */ { /* Load up gene bed hash */ int bedRowSize = 0; struct hash *geneHash = hashTsvBy(geneBed, bedIx, &bedRowSize); int name2Ix = (bedIx == 3 ? bedRowSize-1 : 3); verbose(2, "%d columns about %d genes in %s\n", bedRowSize, geneHash->elCount, geneBed); /* Open up matrix file and read first line into sample labeling */ struct lineFile *lf = lineFileOpen(matrixTsv, TRUE); char *line; lineFileNeedNext(lf, &line, NULL); if (line[0] == '#') // Opening sharp on labels is optional, skip it if there line = skipLeadingSpaces(line+1); int colCount = chopByChar(line, '\t', NULL, 0); int colAlloc = colCount + 1; char **sampleNames; AllocArray(sampleNames, colAlloc); chopByChar(line, '\t', sampleNames, colCount); /* Output sample names and maybe other stuff to trackDb output */ if (trackDb != NULL) { char name[FILENAME_LEN]; splitPath(output, NULL, name, NULL); writeBarChartTrack(trackDb, statsFile, name, colCount-1, sampleNames+1); } /* Open output */ FILE *f = mustOpen(output, "w"); /* Set up row for reading one row of matrix at a time. */ char **matrixRow; AllocArray(matrixRow, colAlloc); int hitCount = 0, missCount = 0; for (;;) { /* Fetch next line and remember how long it is. Just skip over lines that are empty or * start with # character. */ int lineLength = 0; char *line; if (!lineFileNext(lf, &line, &lineLength)) break; char *s = skipLeadingSpaces(line); char c = s[0]; if (c == 0 || c == '#') continue; /* Chop it into tabs */ int rowSize = chopByChar(line, '\t', matrixRow, colAlloc); lineFileExpectWords(lf, colCount, rowSize); char *geneName = matrixRow[0]; struct hashEl *onePos = hashLookup(geneHash, geneName); if (onePos == NULL) { verbose(2, "Can't find gene %s in %s", geneName, geneBed); ++missCount; continue; } else { ++hitCount; } /* A gene may map multiple places. This loop takes care of that */ for (; onePos != NULL; onePos = hashLookupNext(onePos)) { char **geneBedVal = onePos->val; // Get our bed as string array out of hash /* Output info - first six from the bed, then name2, then our barchart */ int i; for (i=0; i<6; ++i) fprintf(f, "%s\t", geneBedVal[i]); char *name2 = geneBedVal[name2Ix]; fprintf(f, "%s\t", name2); /* Print out number of expression values, and comma-sep-list of values themselves. */ fprintf(f, "%d\t", colCount-1); // -1 for skipping label fprintf(f, "%s", matrixRow[1]); for (i=2; i<colCount; ++i) fprintf(f, ",%s", matrixRow[i]); fprintf(f, "\n"); } } carefulClose(&f); verbose(1, "%d genes found, %d (%0.2f%%) missed\n", hitCount, missCount, 100.0*missCount/(hitCount+missCount)); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); clBedIx = optionInt("bedIx", clBedIx); char *trackDb = optionVal("trackDb", NULL); char *stats = optionVal("stats", NULL); matrixToBarChartBed(argv[1], argv[2], stats, argv[3], clBedIx-1, trackDb); return 0; }