2a58331d892e73c2c4969455f750a7b0a41f3ba1 kate Thu Apr 4 16:43:45 2019 -0700 Extend right label feature to show count of cell types contributing to cluster, and total experiments for the factor (configurable). refs #21139 diff --git src/hg/hgTracks/factorSource.c src/hg/hgTracks/factorSource.c index 0e955dc..223277a 100644 --- src/hg/hgTracks/factorSource.c +++ src/hg/hgTracks/factorSource.c @@ -13,63 +13,76 @@ #include "hgTracks.h" #include "expRecord.h" #include "dystring.h" #include "factorSource.h" #include "bed6FloatScore.h" static struct factorSource *loadOne(char **row) /* Load up factorSource from array of strings. */ { return factorSourceLoad(row); } /* Save info about factors and their motifs */ struct factorSourceInfo { boolean showCellAbbrevs; - boolean showCellCounts; + boolean showExpCounts; + struct hash *factorExpCounts; struct hash *factorChoices; struct hash *motifTargets; struct bed6FloatScore *motifs; }; boolean factorFilter(struct track *track, void *item) /* Returns true if an item should be passed by the filter. NOTE: single filter supported here*/ { struct hash *factorHash = ((struct factorSourceInfo *)track->extraUiData)->factorChoices; if (track->extraUiData != NULL && factorHash != NULL) if (hashLookup(factorHash, ((struct factorSource *)item)->name) != NULL) return TRUE; return FALSE; } static void factorSourceLoadItems(struct track *track) /* Load all items (and motifs if table is present) in window */ { bedLoadItem(track, track->table, (ItemLoader)loadOne); if (track->items == NULL) return; struct factorSourceInfo *fsInfo = NULL; AllocVar(fsInfo); track->extraUiData = fsInfo; // Check UI setting to show cell abbreviations or counts char varName[64]; safef(varName, sizeof(varName), "%s.showCellAbbrevs", track->track); fsInfo->showCellAbbrevs = cartUsualBoolean(cart, varName, TRUE); -safef(varName, sizeof(varName), "%s.showCellCounts", track->track); -fsInfo->showCellCounts = cartUsualBoolean(cart, varName, TRUE); +safef(varName, sizeof(varName), "%s.showExpCounts", track->track); +fsInfo->showExpCounts = cartUsualBoolean(cart, varName, FALSE); + +if (fsInfo->showExpCounts) + { + struct sqlConnection *conn = hAllocConn(database); + char query[256]; + char *inputTrackTable = trackDbRequiredSetting(track->tdb, "inputTrackTable"); + sqlSafef(query, sizeof(query), + "select factor, count(*) as num from %s group by factor", inputTrackTable); + fsInfo->factorExpCounts = sqlQuickHash(conn, query); + // TODO: If we're worried about performance, can remake as hash of ints + hFreeConn(&conn); + } // Filter factors based on multi-select filterBy_t *filter = filterBySetGet(track->tdb, cart, NULL); if (filter != NULL && filter->slChoices != NULL && differentString(filter->slChoices->name, "All")) { struct slName *choice; struct hash *factorHash = newHash(0); for (choice = filter->slChoices; choice != NULL; choice = choice->next) { hashAdd(factorHash, choice->name, NULL); } fsInfo->factorChoices = factorHash; filterItems(track, factorFilter, "include"); } @@ -117,71 +130,109 @@ struct hash *targetHash = newHash(0); while ((row = sqlNextRow(sr)) != NULL) { char *target = row[0]; char *motifs = row[1]; // string, comma-sep list, or empty string if (motifs[0] != 0) hashAdd(targetHash, target, slNameListFromString(motifs, ',')); } sqlFreeResult(&sr); fsInfo->motifTargets = targetHash; } } hFreeConn(&conn); } -static int rightPixels(struct track *track, void *item) +static int factorSourceRightPixels(struct track *track, void *item) /* Return number of pixels we need to the right. */ { +struct factorSourceInfo *fsInfo = (struct factorSourceInfo *)track->extraUiData; + +// can we test this here ? +#ifdef BETTER_LAYOUT +if (!(vis == tvFull || vis == tvPack)) + return 0; +#endif struct factorSource *fs = item; struct dyString *dy = dyStringNew(0); +if (fsInfo->showExpCounts) + { + dyStringPrintf(dy, "%d", fs->expCount); + char *s = hashFindVal(fsInfo->factorExpCounts, fs->name); + int allCount = s ? sqlUnsigned(s) : 0; + if (fs->expCount != allCount) + dyStringPrintf(dy, "/%d", allCount); + if (fsInfo->showCellAbbrevs) + dyStringAppend(dy, " "); + } + +if (fsInfo->showCellAbbrevs) + { int i; for (i=0; i<fs->expCount; ++i) { int expNum = fs->expNums[i]; char *label = track->sources[expNum]->name; dyStringAppend(dy, label); } + } int result = mgFontStringWidth(tl.font, dy->string); dyStringFree(&dy); return result; } static void factorSourceDrawItemAt(struct track *track, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw factorSource item at a particular position. */ { /* Figure out maximum score and draw box based on it. */ struct factorSource *fs = item; int grayIx = grayInRange(fs->score, 0, 1000); color = shadesOfGray[grayIx]; /* Calculate position, and draw box around where we are. */ int heightPer = track->heightPer; int x1 = round((double)((int)fs->chromStart-winStart)*scale) + xOff; int x2 = round((double)((int)fs->chromEnd-winStart)*scale) + xOff; int w = x2-x1; if (w < 1) w = 1; hvGfxBox(hvg, x1, y, w, heightPer, color); +if (vis != tvFull && vis != tvPack) + return; /* Draw text to the right */ +int x = x2 + tl.mWidth/2; struct factorSourceInfo *fsInfo = (struct factorSourceInfo *)track->extraUiData; -if ((vis == tvFull || vis == tvPack) && fsInfo->showCellAbbrevs) +if (fsInfo->showExpCounts) + { + struct dyString *ds = dyStringNew(0); + dyStringPrintf(ds, "%d", fs->expCount); + char *s = hashFindVal(fsInfo->factorExpCounts, fs->name); + int allCount = s ? sqlUnsigned(s) : 0; + if (fs->expCount != allCount) + dyStringPrintf(ds, "/%d", allCount); + if (fsInfo->showCellAbbrevs) + dyStringAppend(ds, " "); + char *label = dyStringCannibalize(&ds); + int w = mgFontStringWidth(font, label); + hvGfxTextCentered(hvg, x, y, w, heightPer, MG_BLACK, font, label); + x += w; + } +if (fsInfo->showCellAbbrevs) { - int x = x2 + tl.mWidth/2; int i; for (i=0; i<fs->expCount; ++i) { int id = fs->expNums[i]; char *label = track->sources[id]->name; int w = mgFontStringWidth(font, label); float score = fs->expScores[i]; int grayIx = grayInRange(score, 0, 1000); int color = shadesOfGray[grayIx]; hvGfxTextCentered(hvg, x, y, w, heightPer, color, font, label); x += w; } } } @@ -283,37 +334,39 @@ withLeftLabels = FALSE; genericDrawItems(track, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); withLeftLabels = saveWithLeftLabels; } void factorSourceMethods(struct track *track) /* Set up special methods for factorSource type tracks. */ { /* Start out as a bed, and then specialize loader, mark self as packable. */ track->bedSize = 5; bedMethods(track); track->drawItemAt = factorSourceDrawItemAt; track->drawItems = factorSourceDraw; track->loadItems = factorSourceLoadItems; -track->itemRightPixels = rightPixels; +track->itemRightPixels = factorSourceRightPixels; /* Get the associated data describing the various sources. */ track->expTable = trackDbRequiredSetting(track->tdb, SOURCE_TABLE); struct sqlConnection *conn = hAllocConn(database); char query[256]; track->sourceCount = sqlTableSizeIfExists(conn, track->expTable); sqlSafef(query, sizeof(query), "select * from %s order by id", track->expTable); struct expRecord *exp, *expList = expRecordLoadByQuery(conn, query); int expIx; AllocArray(track->sources, track->sourceCount); for (exp=expList, expIx=0; exp != NULL; exp = exp->next, expIx += 1) track->sources[expIx] = exp; hFreeConn(&conn); /* Figure out how many pixels need to the right. */ +#ifdef UNUSED int rightCount = tl.mWidth/2; for (expIx=0; expIx < track->sourceCount; ++expIx) rightCount += mgFontStringWidth(tl.font, track->sources[expIx]->name); track->sourceRightPixels = rightCount; +#endif }