61e5c823d922898c2774dd7de5231b85d61f306f kent Sat Mar 19 10:24:06 2011 -0700 Adding link to antibody page for factor in TFBS details. Adding cell letter abbreviation column. diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c index 3f8eaae..eb1ff69 100644 --- src/hg/hgc/peakClusters.c +++ src/hg/hgc/peakClusters.c @@ -1,471 +1,485 @@ /* Stuff to display details on tracks that are clusters of peaks (items) in other tracks. * In particular peaks in either ENCODE narrowPeak or broadPeak settings, and residing in * composite tracks. * * These come in two main forms currently: * DNAse hypersensitive clusters - peaks clustered across cell lines stored in bed 5 * with no special type * Transcription Factor Binding Sites (TFBS) - peaks from transcription factor ChIP-seq * across a number of transcription factors and cell lines. Stored in bed 15 * plus sourceTable with type factorSource */ #include "common.h" #include "hash.h" #include "jksql.h" #include "obscure.h" #include "hCommon.h" #include "hdb.h" #include "web.h" #include "cart.h" #include "trackDb.h" #include "hui.h" #include "hgc.h" #include "encode/encodePeak.h" #include "expRecord.h" #include "bed6FloatScore.h" #include "txCluster.h" char *findGroupTagVal(struct trackDb *tdb, char *tag) /* Find value of given tag inside of subgroups field. */ { char *subGroups = trackDbSetting(tdb, "subGroups"); struct slPair *el, *list = slPairFromString(subGroups); char *val = NULL; for (el = list; el != NULL; el = el->next) { if (sameString(el->name, tag)) { val = el->val; break; } } return val; } char *mustFindGroupTagVal(struct trackDb *tdb, char *tag) /* Find value of given tag inside of subgroups field or abort with error message. */ { char *val = findGroupTagVal(tdb, tag); if (val == NULL) errAbort("Couldn't find %s in subGroups tag of %s", tag, tdb->track); return val; } char *findGroupLabel(struct trackDb *tdb, char *group) /* Given name of group, ruffle through all subGroupN tags, looking for one that * matches group */ { char *groupId = mustFindGroupTagVal(tdb, group); return compositeGroupLabel(tdb, group, groupId); } static void printClusterTableHeader(struct slName *otherCols, - boolean withDescription, boolean withSignal) + boolean withAbbreviation, boolean withDescription, boolean withSignal) /* Print out header fields table of tracks in cluster */ { webPrintLabelCell("#"); if (withSignal) webPrintLabelCell("signal"); +if (withAbbreviation) + webPrintLabelCell("abr"); struct slName *col; for (col = otherCols; col != NULL; col = col->next) webPrintLabelCell(col->name); if (withDescription) webPrintLabelCell("description"); } static void printTableInfo(struct trackDb *tdb, struct trackDb *clusterTdb, struct slName *displayGroupList) /* Print out info on table. */ { struct slName *displayGroup; for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next) { char *label = findGroupLabel(tdb, displayGroup->name); char *linkedLabel = compositeLabelWithVocabLink(database, tdb, tdb, displayGroup->name, label); webPrintLinkCell(linkedLabel); } webPrintLinkCellStart(); printf("%s ", tdb->longLabel); compositeMetadataToggle(database, tdb, "...", TRUE, FALSE, trackHash); webPrintLinkCellEnd(); } static void showOnePeakOrMiss(struct trackDb *tdb, struct trackDb *clusterTdb, struct encodePeak *peakList, struct slName *displayGroupList, int *pIx) /* Show info on track and peak. Peak may be NULL in which case fewer columns will be printed. */ { struct encodePeak *peak; *pIx += 1; printf("</TR><TR>\n"); webPrintIntCell(*pIx); if (peakList) { webPrintLinkCellRightStart(); printf("%g", peakList->signalValue); for (peak = peakList->next; peak != NULL; peak = peak->next) printf(",%g", peak->signalValue); webPrintLinkCellEnd(); } printTableInfo(tdb, clusterTdb, displayGroupList); } static boolean showMatchingTrack(char *track, struct bed *cluster, struct sqlConnection *conn, struct trackDb *clusterTdb, struct slName *displayGroupList, boolean invert, int *pRowIx) /* put out a line in an html table that describes the given track. */ { struct trackDb *tdb = hashMustFindVal(trackHash, track); boolean result = FALSE; char **row; int rowOffset = 0; struct sqlResult *sr = hRangeQuery(conn, tdb->table, cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, &rowOffset); struct encodePeak *peakList = NULL; struct slDouble *slDoubleNew(double x); while ((row = sqlNextRow(sr)) != NULL) { enum encodePeakType pt = encodePeakInferTypeFromTable(database, tdb->table, tdb->type); struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt); slAddTail(&peakList, peak); } if (invert) { if (!peakList) showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, pRowIx); } else { if (peakList) showOnePeakOrMiss(tdb, clusterTdb, peakList, displayGroupList, pRowIx); } sqlFreeResult(&sr); return result; } static void printClusterTableHits(struct bed *cluster, struct sqlConnection *conn, char *sourceTable, char *inputTrackTable, struct slName *fieldList, boolean invert, char *vocab) /* Put out a lines in an html table that shows assayed sources that have hits in this * cluster, or if invert is set, that have misses. */ { +char *vocabFile = NULL; +if (vocab) + vocabFile = cloneFirstWord(vocab); /* Make the monster SQL query to get all assays*/ struct dyString *query = dyStringNew(0); -dyStringPrintf(query, "select %s.id", sourceTable); +dyStringPrintf(query, "select %s.id,%s.name", sourceTable, sourceTable); struct slName *field; for (field = fieldList; field != NULL; field = field->next) dyStringPrintf(query, ",%s.%s", inputTrackTable, field->name); dyStringPrintf(query, " from %s,%s ", inputTrackTable, sourceTable); dyStringPrintf(query, " where %s.source = %s.description", inputTrackTable, sourceTable); dyStringPrintf(query, " and factor='%s' order by %s.source", cluster->name, inputTrackTable); int displayNo = 0; int fieldCount = slCount(fieldList); struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) { int sourceId = sqlUnsigned(row[0]); double signal = cluster->expScores[sourceId]; boolean hit = (signal > 0); if (hit ^ invert) { printf("</TR><TR>\n"); webPrintIntCell(++displayNo); if (!invert) webPrintDoubleCell(signal); + webPrintLinkCell(row[1]); int i; for (i=0; i<fieldCount; ++i) { - char *fieldVal = row[i+1]; + char *fieldVal = row[i+2]; if (vocab) { - char *file = cloneFirstWord(vocab); - char *link = controlledVocabLink(file, "term", fieldVal, fieldVal, fieldVal, ""); + char *link = controlledVocabLink(vocabFile, "term", + fieldVal, fieldVal, fieldVal, ""); webPrintLinkCell(link); } else webPrintLinkCell(fieldVal); } } } sqlFreeResult(&sr); +freez(&vocabFile); dyStringFree(&query); } static struct slName *findMatchingSubtracks(struct trackDb *tdb) /* Find subtracks that match inputTracks tags. */ { /* Just list look up tableName in inputTrackTable and return the list. */ char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); struct sqlConnection *conn = hAllocConn(database); char query[256]; safef(query, sizeof(query), "select tableName from %s order by source", inputTrackTable); struct slName *matchTrackList = sqlQuickList(conn, query); hFreeConn(&conn); return matchTrackList; } void doPeakClusterListItemsAssayed() /* Put up a page that shows all experiments associated with a cluster track. */ { struct trackDb *clusterTdb = tdbForTableArg(); struct slName *matchTrackList = findMatchingSubtracks(clusterTdb); struct slName *matchTrack; cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel); char *inputTracksSubgroupDisplay = trackDbRequiredSetting(clusterTdb, "inputTracksSubgroupDisplay"); struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); webPrintLinkTableStart(); -printClusterTableHeader(displayGroupList, TRUE, FALSE); +printClusterTableHeader(displayGroupList, FALSE, TRUE, FALSE); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { struct trackDb *tdb = hashFindVal(trackHash, matchTrack->name); showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, &rowIx); } webPrintLinkTableEnd(); cartWebEnd(); } void doPeakClusters(struct trackDb *tdb, char *item) /* Display detailed info about a cluster of peaks from other tracks. */ { int start = cartInt(cart, "o"); char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); char query[256]; struct sqlResult *sr; char **row; struct bed *cluster = NULL; struct sqlConnection *conn = hAllocConn(database); cartWebStart(cart, database, "%s item details", tdb->shortLabel); safef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) cluster = bedLoadN(row + rowOffset, 5); sqlFreeResult(&sr); if (cluster != NULL) { /* Get list of subgroups to display */ char *inputTracksSubgroupDisplay = trackDbRequiredSetting(tdb, "inputTracksSubgroupDisplay"); struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); /* Get list of tracks that match criteria. */ struct slName *matchTrackList = findMatchingSubtracks(tdb); struct slName *matchTrack; /* Print out some information about the cluster overall. */ printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, slCount(matchTrackList)); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); /* In a new section put up list of hits. */ webNewSection("List of Items in Cluster"); webPrintLinkTableStart(); - printClusterTableHeader(displayGroupList, TRUE, TRUE); + printClusterTableHeader(displayGroupList, FALSE, TRUE, TRUE); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, FALSE, &rowIx); } webPrintLinkTableEnd(); } printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(), tdb->track); printf("List all items assayed"); printf("</A><BR>\n"); webNewSection("Track Description"); printTrackHtml(tdb); cartWebEnd(); hFreeConn(&conn); } char *findFactorId(struct slName *trackList, char *label) /* Given factor label, find factor id. */ { struct slName *track; for (track = trackList; track != NULL; track = track->next) { struct trackDb *tdb = hashMustFindVal(trackHash, track->name); char *factorId = compositeGroupId(tdb, "factor", label); if (factorId != NULL) return factorId; } errAbort("Couldn't find factor labeled %s", label); return NULL; } void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display detailed info about a cluster of peaks from other tracks. */ { int rowOffset = hOffsetPastBin(database, seqName, tdb->table); char **row; struct sqlResult *sr; char query[256]; char *motifTable = NULL; #ifdef TXCLUSTER_MOTIFS_TABLE motifTable = TXCLUSTER_MOTIFS_TABLE; #endif safef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); struct bed *cluster = NULL; if (row != NULL) cluster = bedLoadN(row + rowOffset, 15); sqlFreeResult(&sr); if (cluster != NULL) { char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); struct dnaMotif *motif = NULL; struct dnaSeq **seqs = NULL; struct bed6FloatScore *hits = NULL; if(motifTable != NULL && sqlTableExists(conn, motifTable)) { struct sqlResult *sr; int rowOffset; char where[256]; motif = loadDnaMotif(item, "transRegCodeMotif"); safef(where, sizeof(where), "name = '%s'", item); sr = hRangeQuery(conn, "wgEncodeRegTfbsClusteredMotifs", cluster->chrom, cluster->chromStart, cluster->chromEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { struct bed6FloatScore *hit = NULL; AllocVar(hit); hit->chromStart = sqlUnsigned(row[rowOffset + 1]); hit->chromEnd = sqlUnsigned(row[rowOffset + 2]); hit->score = sqlFloat(row[rowOffset + 4]); hit->strand[0] = row[rowOffset + 5][0]; slAddHead(&hits, hit); } sqlFreeResult(&sr); } - printf("<B>Factor:</B> %s<BR>\n", cluster->name); + char *factorLink = cluster->name; + char *vocab = trackDbSetting(tdb, "controlledVocabulary"); + if (vocab != NULL) + { + char *file = cloneFirstWord(vocab); + factorLink = controlledVocabLink(file, "term", factorLink, factorLink, factorLink, ""); + } + printf("<B>Factor:</B> %s<BR>\n", factorLink); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); if(motif != NULL && hits != NULL) { struct bed6FloatScore *hit = NULL; int i; seqs = needMem(sizeof(struct dnaSeq *) * slCount(hits)); for (hit = hits, i = 0; hit != NULL; hit = hit->next, i++) { char query[256]; float maxScore = -1; safef(query, sizeof(query), "select max(score) from %s where name = '%s'", "wgEncodeRegTfbsClusteredMotifs", item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if(!isEmpty(row[0])) { maxScore = sqlFloat(row[0]); } } sqlFreeResult(&sr); struct dnaSeq *seq = hDnaFromSeq(database, seqName, hit->chromStart, hit->chromEnd, dnaLower); if(hit->strand[0] == '-') reverseComplement(seq->dna, seq->size); seqs[i] = seq; printf("<B>Motif Score #%d:</B> %.2f (max: %.2f)<BR>\n", i + 1, hit->score, maxScore); } } printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); if(seqs != NULL) { motifMultipleHitsSection(seqs, slCount(hits), motif); } /* Get list of tracks we'll look through for input. */ char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); safef(query, sizeof(query), "select tableName from %s where factor='%s' order by source", inputTrackTable, cluster->name); struct slName *matchTrackList = sqlQuickList(conn, query); struct slName *matchTrack; /* Next do the lists of hits and misses. We have the hits from the non-zero signals in * cluster->expScores. We need to figure out the sources actually assayed though * some other way. We'll do this by one of two techniques. * If the inputTracksSubgroupDisplay is set, we'll try and figure out what was * assayed by looking at the subgroup stuff in trackDb, which works if everythings * part of a composite. If not, we'll use the inputTrackTable. */ /* Get list of subgroups to display */ char *inputTracksSubgroupDisplay = trackDbSetting(tdb, "inputTracksSubgroupDisplay"); char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay"); if (inputTracksSubgroupDisplay != NULL) { struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); /* In a new section put up list of hits. */ webNewSection("List of %s Items in Cluster", cluster->name); webPrintLinkTableStart(); - printClusterTableHeader(displayGroupList, TRUE, TRUE); + printClusterTableHeader(displayGroupList, FALSE, TRUE, TRUE); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, FALSE, &rowIx); } webPrintLinkTableEnd(); webNewSection("List of cells assayed with %s but without hits in cluster", cluster->name); webPrintLinkTableStart(); - printClusterTableHeader(displayGroupList, TRUE, FALSE); + printClusterTableHeader(displayGroupList, FALSE, TRUE, FALSE); rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, TRUE, &rowIx); } webPrintLinkTableEnd(); } else if (inputTableFieldDisplay != NULL) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); char *vocab = trackDbSetting(tdb, "controlledVocabulary"); /* In a new section put up list of hits. */ webNewSection("List of %s Items in Cluster", cluster->name); webPrintLinkTableStart(); - printClusterTableHeader(fieldList, FALSE, TRUE); + printClusterTableHeader(fieldList, TRUE, FALSE, TRUE); printClusterTableHits(cluster, conn, sourceTable, inputTrackTable, fieldList, FALSE, vocab); webPrintLinkTableEnd(); webNewSection("List of cells assayed with %s but without hits in cluster", cluster->name); webPrintLinkTableStart(); - printClusterTableHeader(fieldList, FALSE, FALSE); + printClusterTableHeader(fieldList, TRUE, FALSE, FALSE); printClusterTableHits(cluster, conn, sourceTable, inputTrackTable, fieldList, TRUE, vocab); webPrintLinkTableEnd(); } else { errAbort("Missing required trackDb setting %s or %s for track %s", "inputTracksSubgroupDisplay", "inputTableFieldDisplay", tdb->track); } webNewSection("Table of abbreviations for cells"); hPrintAbbreviationTable(conn, sourceTable, "Cell Type"); webNewSection("Track Description"); } }