src/hg/hgc/peakClusters.c 1.3
1.3 2010/05/18 00:04:40 kent
Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
Index: src/hg/hgc/peakClusters.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/peakClusters.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/hgc/peakClusters.c 17 May 2010 02:30:20 -0000 1.2
+++ src/hg/hgc/peakClusters.c 18 May 2010 00:04:40 -0000 1.3
@@ -1,259 +1,347 @@
/* 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"
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 *displayGroupList)
-/* Print out header fields table */
+/* Print out header fields table of tracks in cluster */
{
webPrintLabelCell("#");
webPrintLabelCell("signal");
struct slName *displayGroup;
for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next)
{
webPrintLabelCell(displayGroup->name);
}
webPrintLabelCell("description");
printf("</TR><TR>\n");
}
+static void printOutOfClusterTableHeader(struct slName *displayGroupList)
+/* Print out header fields for table of tracks not in cluster */
+{
+webPrintLabelCell("#");
+struct slName *displayGroup;
+for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next)
+ {
+ webPrintLabelCell(displayGroup->name);
+ }
+webPrintLabelCell("description");
+printf("</TR><TR>\n");
+}
+
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);
}
webPrintLinkCell(tdb->longLabel);
}
-static void showOnePeak(struct trackDb *tdb, struct bed *cluster, struct trackDb *clusterTdb,
+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 n/a's will be printed
- * as appropriate. */
+/* Show info on track and peak. Peak may be NULL in which case fewer columns will be printed. */
{
struct encodePeak *peak;
*pIx += 1;
webPrintIntCell(*pIx);
-webPrintLinkCellRightStart();
-printf("%g", peakList->signalValue);
-for (peak = peakList->next; peak != NULL; peak = peak->next)
+if (peakList)
+ {
+ webPrintLinkCellRightStart();
+ printf("%g", peakList->signalValue);
+ for (peak = peakList->next; peak != NULL; peak = peak->next)
printf(",%g", peak->signalValue);
-webPrintLinkCellEnd();
+ webPrintLinkCellEnd();
+ }
printTableInfo(tdb, clusterTdb, displayGroupList);
printf("</TR><TR>\n");
}
static boolean showMatchingTrack(char *track, struct bed *cluster, struct sqlConnection *conn,
- struct trackDb *clusterTdb, struct slName *displayGroupList, int *pRowIx)
+ 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 (peakList)
- showOnePeak(tdb, cluster, clusterTdb, peakList, displayGroupList, pRowIx);
+if (invert)
+ {
+ if (!peakList)
+ showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, pRowIx);
+ }
+else
+ {
+ if (peakList)
+ showOnePeakOrMiss(tdb, clusterTdb, peakList, displayGroupList, pRowIx);
+ }
sqlFreeResult(&sr);
return result;
}
+static struct slName *findMatchingSubtracks(struct trackDb *tdb)
+/* Find subtracks that match inputTracks tags. */
+{
+/* Get list of tracks we'll look through for input. */
+char *inputTracks = trackDbRequiredSetting(tdb, "inputTracks");
+struct slName *inTrackList = stringToSlNames(inputTracks);
+
+/* Get list of subgroups to select on */
+char *inputTracksSubgroupSelect = trackDbRequiredSetting(tdb, "inputTracksSubgroupSelect");
+struct slPair *selGroupList = slPairFromString(inputTracksSubgroupSelect);
+
+struct slName *matchTrackList = encodeFindMatchingSubtracks(inTrackList, selGroupList);
+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;
+
+char title[256];
+safef(title, sizeof(title), "List of items assayed in %s", clusterTdb->shortLabel);
+cartWebStart(cart, database, title);
+
+char *inputTracksSubgroupDisplay = trackDbRequiredSetting(clusterTdb, "inputTracksSubgroupDisplay");
+struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay);
+webPrintLinkTableStart();
+printOutOfClusterTableHeader(displayGroupList);
+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();
+}
+
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);
char title[256];
safef(title, sizeof(title), "%s item details", tdb->shortLabel);
cartWebStart(cart, database, title);
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 tracks we'll look through for input. */
- char *inputTracks = trackDbRequiredSetting(tdb, "inputTracks");
- struct slName *inTrackList = stringToSlNames(inputTracks);
-
- /* Get list of subgroups to select on */
- char *inputTracksSubgroupSelect = trackDbRequiredSetting(tdb, "inputTracksSubgroupSelect");
- struct slPair *selGroupList = slPairFromString(inputTracksSubgroupSelect);
-
/* 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 = encodeFindMatchingSubtracks(inTrackList, selGroupList);
+ 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);
int rowIx = 0;
for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
{
showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList,
- &rowIx);
+ FALSE, &rowIx);
}
webPrintLinkTableEnd();
}
+printf("<A HREF=\"%s&g=hgcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(),
+ tdb->track);
+printf("List all items assayed");
webNewSection("Track Description");
+printf("</A><BR>\n");
printTrackHtml(tdb);
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];
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)
{
printf("<B>Factor:</B> %s<BR>\n", cluster->name);
printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable");
uglyf("<B>sourceTable:</B> %s<BR>\n", sourceTable);
/* Get list of tracks we'll look through for input. */
char *inputTracks = trackDbRequiredSetting(tdb, "inputTracks");
struct slName *inTrackList = stringToSlNames(inputTracks);
uglyf("<B>inputTracks:</B> %s (%d)<BR>\n", inputTracks, slCount(inTrackList));
/* Get list of subgroups to select on */
char *inputTracksSubgroupSelect = trackDbRequiredSetting(tdb, "inputTracksSubgroupSelect");
struct slPair *selGroupList = slPairFromString(inputTracksSubgroupSelect);
uglyf("<B>inputTracksSubgroupSelect:</B> %s (%d)<BR>\n", inputTracksSubgroupSelect, slCount(selGroupList));
+ /* Get list of subgroups to display */
+ char *inputTracksSubgroupDisplay = trackDbRequiredSetting(tdb, "inputTracksSubgroupDisplay");
+ struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay);
+
/* Figure out factor ID and add it as selection criteria*/
char *factorId = findFactorId(inTrackList, cluster->name);
uglyf("<B>cluster->id:</B> %s <B>factorId:</B> %s<BR>\n", cluster->name, factorId);
struct slPair *factorSel = slPairNew("factor", cloneString(factorId));
slAddHead(&selGroupList, factorSel);
/* Get list of tracks that match criteria. */
struct slName *matchTrackList = encodeFindMatchingSubtracks(inTrackList, selGroupList);
- // struct slName *matchTrack;
+ struct slName *matchTrack;
uglyf("<B>matchTrackList:</B> %d elements<BR>\n", slCount(matchTrackList));
+ /* In a new section put up list of hits. */
+ webNewSection("List of %s Items in Cluster", cluster->name);
+ webPrintLinkTableStart();
+ printClusterTableHeader(displayGroupList);
+ 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();
+ printOutOfClusterTableHeader(displayGroupList);
+ rowIx = 0;
+ for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
+ {
+ showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList,
+ TRUE, &rowIx);
+ }
+ webPrintLinkTableEnd();
+
+ webNewSection("Track Description");
}
}