0451226a890984e2b9dc9a7902d41014c3e24c66 aamp Mon May 23 17:13:43 2011 -0700 some lines I needed to NOT break the build. hgTrackUi and hgTracks were updated but not hgc diff --git src/hg/hgc/expClick.c src/hg/hgc/expClick.c index 191d0e0..be9bc54 100644 --- src/hg/hgc/expClick.c +++ src/hg/hgc/expClick.c @@ -1,487 +1,491 @@ /* Handle details pages for expression ratio tracks. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "hgc.h" #include "hui.h" #include "expRecord.h" #include "obscure.h" #include "cheapcgi.h" #include "genePred.h" #include "affyAllExonProbe.h" #include "microarray.h" static char const rcsid[] = "$Id: expClick.c,v 1.25 2010/05/11 01:43:28 kent Exp $"; /* global flag to indicate if the track is a cancer genomics track */ boolean isCancerGenomicsTrack = FALSE; static struct rgbColor getColorForExprBed(float val, float max, enum expColorType colorScheme) /* Return the correct color for a given score */ { float absVal = fabs(val); struct rgbColor color; int colorIndex = 0; /* if log score is -10000 data is missing */ if(val == -10000) { color.g = color.r = color.b = 128; return(color); } if(absVal > max) absVal = max; if (max == 0) errAbort("ERROR: hgc::getColorForExprBed() maxDeviation can't be zero\n"); colorIndex = (int)(absVal * 255/max); color.r = color.g = color.b = 0; if (colorScheme == redBlue) if (val > 0) color.r = colorIndex; else color.b = colorIndex; else if (colorScheme == yellowBlue) if (val > 0) { color.r = colorIndex; color.g = colorIndex; } else color.b = colorIndex; else if (colorScheme == redBlueOnWhite) if (val > 0) { color.r = 255; color.g = 255 - colorIndex; color.b = 255 - colorIndex; } else { color.r = 255 - colorIndex; color.g = 255 - colorIndex; color.b = 255; } else if (colorScheme == redBlueOnYellow) if (val > 0) { color.r = 255; color.g = 255 - colorIndex; } else { color.r = 255 - colorIndex; color.g = 255 - colorIndex; color.b = colorIndex; } else if (val > 0) color.r = colorIndex; else color.g = colorIndex; return color; } static void msBedPrintTableHeader(struct bed *bedList, struct hash *erHash, char *itemName, char **headerNames, int headerCount, char *scoresHeader) /* print out a bed with multiple scores header for a table. headerNames contain titles of columns up to the scores columns. scoresHeader is a single string that will span as many columns as there are beds.*/ { struct bed *bed; int featureCount = slCount(bedList); int i=0; printf("<tr>"); for(i=0;i<headerCount; i++) printf("<th align=center>%s</th>\n",headerNames[i]); printf("<th align=center colspan=%d valign=top>%s</th>\n",featureCount, scoresHeader); printf("</tr>\n<tr>"); for(i=0;i<headerCount; i++) printf("<td> </td>\n"); for(bed = bedList; bed != NULL; bed = bed->next) { printf("<td valign=top align=center>\n"); printTableHeaderName(bed->name, itemName, NULL); printf("</td>"); } printf("</tr>\n"); } static void msBedDefaultPrintHeader(struct bed *bedList, struct hash *erHash, char *itemName) /* print out a header with names for each bed with itemName highlighted */ { char *headerNames[] = {"Experiment"}; char *scoresHeader = "Item Name"; msBedPrintTableHeader(bedList, erHash, itemName, headerNames, ArraySize(headerNames), scoresHeader); } static void printExprssnColorKey(float minVal, float maxVal, float stepSize, int base, struct rgbColor(*getColor)(float val, float maxVal, enum expColorType colorScheme), enum expColorType colorScheme) /* print out a little table which provides a color->score key */ { float currentVal = -1 * maxVal; int numColumns; assert(stepSize != 0); numColumns = maxVal/stepSize *2+1; printf("<TABLE BGCOLOR=\"#000000\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>"); printf("<TABLE BGCOLOR=\"#fffee8\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR>"); printf("<th colspan=%d>False Color Key, all values log base %d</th></tr><tr>\n",numColumns, base); /* have to add the stepSize/2 to account for the ability to absolutely represent some numbers as floating points */ for(currentVal = minVal; currentVal <= maxVal + (stepSize/2); currentVal += stepSize) { printf("<th><b>%.1f </b></th>", currentVal); } printf("</tr><tr>\n"); for(currentVal = minVal; currentVal <= maxVal + (stepSize/2); currentVal += stepSize) { struct rgbColor rgb = getColor(currentVal, maxVal, colorScheme); printf("<td bgcolor=\"#%.2X%.2X%.2X\"> </td>\n", rgb.r, rgb.g, rgb.b); } printf("</tr></table>\n"); printf("</td></tr></table>\n"); } static void msBedExpressionPrintRow(struct bed *bedList, struct hash *erHash, int expIndex, char *expName, float maxScore, enum expColorType colorScheme) /* print the name of the experiment and color the background of individual cells using the score to create false two color display */ { char buff[32]; struct bed *bed = bedList; struct expRecord *er = NULL; int square = 10; snprintf(buff, sizeof(buff), "%d", expIndex); er = hashMustFindVal(erHash, buff); printf("<tr>\n"); if(strstr(er->name, expName)) printf("<td align=left bgcolor='#D9E4F8'> %s</td>\n",er->name); else { if (isCancerGenomicsTrack) { printf("<td align=left><A HREF=\"../cgi-bin/subjectView?sv_dataset=%s&sv_subjectId=%s\" TARGET=_blank>%s</A></td>\n", cartString(cart, "g"), er->name, er->name); } else { printf("<td align=left> %s</td>\n", er->name); } } for(bed = bedList;bed != NULL; bed = bed->next) { /* use the background colors to creat patterns */ struct rgbColor rgb = getColorForExprBed(bed->expScores[expIndex], maxScore, colorScheme); printf("<td height=%d width=%d bgcolor=\"#%.2X%.2X%.2X\"> </td>\n", square, square, rgb.r, rgb.g, rgb.b); } printf("</tr>\n"); } static void msBedPrintTable(struct bed *bedList, struct hash *erHash, char *itemName, char *expName, float minScore, float maxScore, float stepSize, int base, void(*printHeader)(struct bed *bedList, struct hash *erHash, char *item), void(*printRow)(struct bed *bedList,struct hash *erHash, int expIndex, char *expName, float maxScore, enum expColorType colorScheme), void(*printKey)(float minVal, float maxVal, float size, int base, struct rgbColor(*getColor)(float val, float max, enum expColorType colorScheme), enum expColorType colorScheme), struct rgbColor(*getColor)(float val, float max, enum expColorType colorScheme), enum expColorType colorScheme) /* prints out a table from the data present in the bedList */ { int i,featureCount=0; if(bedList == NULL) errAbort("hgc::msBedPrintTable() - bedList is NULL"); featureCount = slCount(bedList); /* time to write out some html, first the table and header */ if(printKey != NULL) printKey(minScore, maxScore, stepSize, base, getColor, colorScheme); printf("<p>\n"); printf("<basefont size=-1>\n"); printf("<table bgcolor=\"#000000\" border=\"0\" cellspacing=\"0\" cellpadding=\"1\"><tr><td>"); printf("<table bgcolor=\"#fffee8\" border=\"0\" cellspacing=\"0\" cellpadding=\"1\">"); printHeader(bedList, erHash, itemName); for(i=0; i<bedList->expCount; i++) { printRow(bedList, erHash, i, expName, maxScore, colorScheme); } printf("</table>"); printf("</td></tr></table>"); printf("</basefont>"); } static struct bed *loadMsBed(struct trackDb *tdb, char *table, char *chrom, uint start, uint end) /* load every thing from a bed 15 table in the given range */ { struct sqlConnection *conn = hAllocConnTrack(database, tdb); struct sqlResult *sr; char **row; int rowOffset; struct bed *bedList = NULL, *bed; sr = hRangeQuery(conn, table, chrom, start, end, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+rowOffset, 15); slAddHead(&bedList, bed); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&bedList); return bedList; } static struct bed * loadMsBedAll(char *table) /* load every thing from a bed 15 table */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct bed *bedList = NULL, *bed; char query[512]; sprintf(query, "select * from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row, 15); slAddHead(&bedList, bed); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&bedList); return bedList; } static struct expRecord * loadExpRecord(char *table, char *database) /* load everything from an expRecord table in the specified database, usually hgFixed instead of hg7, hg8, etc. */ { struct sqlConnection *conn = sqlConnect(database); char query[256]; struct expRecord *erList = NULL; snprintf(query, sizeof(query), "select * from %s", table); erList = expRecordLoadByQuery(conn, query); sqlDisconnect(&conn); return erList; } void getMsBedExpDetails(struct trackDb *tdb, char *expName, boolean all) /* Create tab-delimited output to download */ { char *expTable = cartString(cart, "i"); char *bedTable = cartString(cart, "o"); struct expRecord *er, *erList=NULL; struct bed *b, *bedList=NULL; int i; /* Get all of the expression record details */ erList = loadExpRecord(expTable, "hgFixed"); /* Get either all of the data, or only that data in the range */ if (all) bedList = loadMsBedAll(bedTable); else bedList = loadMsBed(tdb, bedTable, seqName, winStart, winEnd); /* Print out a header row */ printf("<HTML><BODY><PRE>\n"); printf("Name\tChr\tChrStart\tChrEnd\tTallChrStart\tTallChrEnd"); for (er = erList; er != NULL; er = er->next) if (sameString(bedTable, "cghNci60")) printf("\t%s(%s)",er->name, er->extras[1]); else printf("\t%s",er->name); printf("\n"); /* Print out a row for each of the record in the bedList */ for (b = bedList; b != NULL; b = b->next) { printf("%s\t%s\t%d\t%d\t%d\t%d",b->name, b->chrom, b->chromStart, b->chromEnd, b->thickStart, b->thickEnd); for (i = 0; i < b->expCount; i++) if (i == b->expIds[i]) printf("\t%f",b->expScores[i]); else printf("\t"); printf("\n"); } printf("</PRE>"); } struct expRecord *basicExpRecord(char *expName, int id, int extrasIndex) /* This returns a stripped-down new expRecord, probably the result of an average. */ { int i; struct expRecord *er = NULL; AllocVar(er); er->id = id; er->name = cloneString(expName); er->description = cloneString(expName); er->url = cloneString("n/a"); er->ref = cloneString("n/a"); er->credit = cloneString("n/a"); er->numExtras = extrasIndex+1; AllocArray(er->extras, er->numExtras); for (i = 0; i < er->numExtras; i++) er->extras[i] = cloneString(expName); return er; } void bedListExpRecordAverage(struct bed **pBedList, struct expRecord **pERList, int extrasIndex) /* This is a mildy complicated function to make the details page have the */ /* same data as the track when the UI option "Tissue averages" is selected. */ /* This is done by hacking the bed and expRecord lists in place and keeping */ /* the original code for the most part. */ { struct bed *bed = NULL; struct expRecord *er, *newERList = NULL; struct slName *extras = NULL, *oneSlName; int M, N, i, columns; int *mapping; if (!pBedList || !pERList || !*pBedList || !*pERList) return; er = *pERList; if ((extrasIndex < 0) || (extrasIndex >= er->numExtras)) return; /* Build up a unique list of words from the specific "extras" column. */ for (er = *pERList; er != NULL; er = er->next) slNameStore(&extras, er->extras[extrasIndex]); slReverse(&extras); M = slCount(extras); N = slCount(*pERList); columns = N + 1; /* M rows, reserve first column for counts. */ mapping = needMem(sizeof(int) * M * columns); /* Create the mapping array: */ /* each row corresponds to one of the groupings. The first column is the number of */ /* things in the original list in the group (k things), and the next k elements on */ /* that row are indeces. */ for (er = *pERList, i = 0; er != NULL && i < N; er = er->next, i++) { int ix = slNameFindIx(extras, er->extras[extrasIndex]) * columns; mapping[ix + ++mapping[ix]] = er->id; } /* Make a new expRecord list. */ for (oneSlName = extras, i = 0; oneSlName != NULL && i < M; oneSlName = oneSlName->next, i++) { struct expRecord *newER = basicExpRecord(oneSlName->name, i, extrasIndex); slAddHead(&newERList, newER); } slReverse(&newERList); expRecordFreeList(pERList); *pERList = newERList; /* Go through each bed and change it. */ for (bed = *pBedList; bed != NULL; bed = bed->next) { float *newExpScores = needMem(sizeof(float) * M); int *newExpIds = needMem(sizeof(int) * M); /* Calculate averages. */ for (i = 0; i < M; i++) { int ix = i * columns; int size = mapping[ix]; int j; double sum = 0; for (j = 1; j < size + 1; j++) sum += (double)bed->expScores[mapping[ix + j]]; newExpScores[i] = (float)(sum/size); newExpIds[i] = i; } bed->expCount = M; freeMem(bed->expIds); bed->expIds = newExpIds; freeMem(bed->expScores); bed->expScores = newExpScores; } /* Free stuff. */ slNameFreeList(&extras); freez(&mapping); } void erHashElFree(struct hashEl *el) /* Frees up expRecord hash head. */ { struct expRecord *er = el->val; expRecordFree(&er); } void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct) /* Generic expression ratio deatils using microarrayGroups.ra file */ /* and not the expRecord tables. */ { char *expScale = trackDbRequiredSetting(tdb, "expScale"); char *expStep = trackDbRequiredSetting(tdb, "expStep"); double maxScore = atof(expScale); double stepSize = atof(expStep); struct bed *bedList; char *itemName = cgiUsualString("i2","none"); char *expName = (item == NULL) ? itemName : item; char *tdbSetting = trackDbSettingOrDefault(tdb, "expColor", "redGreen"); char *colorVal = NULL; enum expColorType colorScheme; char colorVarName[256]; safef(colorVarName, sizeof(colorVarName), "%s.color", tdb->track); colorVal = cartUsualString(cart, colorVarName, tdbSetting); colorScheme = getExpColorType(colorVal); if (sameWord(tdb->grp, "cancerGenomics")) { /* set global flag */ isCancerGenomicsTrack = TRUE; } if (!ct) { genericHeader(tdb, itemName); bedList = loadMsBed(tdb, tdb->table, seqName, winStart, winEnd); } else if (ct->dbTrack) { genericHeader(tdb, itemName); printCustomUrl(tdb, itemName, TRUE); bedList = ctLoadMultScoresBedDb(ct, seqName, winStart, winEnd); } else bedList = bedFilterListInRange(ct->bedList, NULL, seqName, winStart, winEnd); if (bedList == NULL) printf("<b>No Expression Data in this Range.</b>\n"); else if (expName && sameString(expName, "zoomInMore")) printf("<b>Too much data to display in detail in this range.</b>\n"); else { struct microarrayGroups *groupings = NULL; struct maGrouping *combineGroup; + struct maGrouping *subset = NULL; + int subsetOffset = -1; struct hash *erHash = newHash(6); int i; if (!ct) { groupings = maGetTrackGroupings(database, tdb); combineGroup = maCombineGroupingFromCart(groupings, cart, tdb->track); + subset = maSubsetGroupingFromCart(groupings, cart, tdb->track); + subsetOffset = maSubsetOffsetFromCart(subset, cart, tdb->track); } else combineGroup = maGetGroupingFromCt(ct); - maBedClumpGivenGrouping(bedList, combineGroup); + maBedClumpGivenGrouping(bedList, combineGroup, subset, subsetOffset); for (i = 0; i < combineGroup->numGroups; i++) { /* make stupid exprecord hash.perhaps eventually this won't be needed */ char id[16]; struct expRecord *er = basicExpRecord(combineGroup->names[i], i, 2); safef(id, sizeof(id), "%d", i); hashAdd(erHash, id, er); } puts("<h2></h2><p>\n"); msBedPrintTable(bedList, erHash, itemName, expName, -1*maxScore, maxScore, stepSize, 2, msBedDefaultPrintHeader, msBedExpressionPrintRow, printExprssnColorKey, getColorForExprBed, colorScheme); hashTraverseEls(erHash, erHashElFree); hashFree(&erHash); microarrayGroupsFree(&groupings); } puts("<h2></h2><p>\n"); bedFreeList(&bedList); }