a15e95bf88dc310df10549c6bb17c288654aad64 kate Wed Oct 25 10:58:43 2017 -0700 Fix filter problem noted in RM note #77; effect and prob filters should change item label to correspond to eQTLs remaining in combined item after filtering. refs #15646 diff --git src/hg/hgTracks/gtexEqtlClusterTrack.c src/hg/hgTracks/gtexEqtlClusterTrack.c index 73d1f03..9471dc6 100644 --- src/hg/hgTracks/gtexEqtlClusterTrack.c +++ src/hg/hgTracks/gtexEqtlClusterTrack.c @@ -1,330 +1,337 @@ /* gtexEqtlClusterTrack - Track of clustered expression QTL's from GTEx */ /* Copyright (C) 2017 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "dystring.h" #include "hgTracks.h" #include "gtexInfo.h" #include "gtexTissue.h" #include "gtexUi.h" #include "gtexEqtlCluster.h" struct gtexEqtlClusterTrack /* Track info for filtering (maybe later for draw, map) */ { struct gtexTissue *tissues; /* Tissue names, descriptions */ struct hash *tissueHash; /* Tissue info, keyed by UCSC name, filtered by UI */ boolean doTissueColor; /* Display tissue color (for single-tissue eQTL's) */ double minEffect; /* Effect size filter (abs value) */ double minProb; /* Probability filter */ }; /* Utility functions */ static struct gtexEqtlCluster *loadOne(char **row) /* Load up gtexEqtlCluster from array of strings. */ { return gtexEqtlClusterLoad(row); } static boolean filterTissuesFromCart(struct track *track, struct gtexEqtlClusterTrack *extras) /* Check cart for tissue selection. Populate track tissues hash */ { char *version = gtexVersionSuffix(track->table); extras->tissues = gtexGetTissues(version); extras->tissueHash = hashNew(0); struct gtexTissue *tis = NULL; for (tis = extras->tissues; tis != NULL; tis = tis->next) hashAdd(extras->tissueHash, tis->name, tis); // if all tissues included, return full hash if (!cartListVarExistsAnyLevel(cart, track->tdb, FALSE, GTEX_TISSUE_SELECT)) return FALSE; struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, track->tdb, FALSE, GTEX_TISSUE_SELECT); if (selectedValues == NULL || slCount(selectedValues) == slCount(extras->tissues)) return FALSE; // create tissue hash with only included tissues struct hash *tisHash = hashNew(0); struct slName *name; for (name = selectedValues; name != NULL; name = name->next) { tis = (struct gtexTissue *)hashFindVal(extras->tissueHash, name->name); if (tis != NULL) hashAdd(tisHash, name->name, tis); } extras->tissueHash = tisHash; return TRUE; } static void eqtlExcludeTissue(struct gtexEqtlCluster *eqtl, int i) /* Mark the tissue to exclude from display */ { eqtl->expScores[i] = 0.0; } static boolean eqtlIsExcludedTissue(struct gtexEqtlCluster *eqtl, int i) /* Check if eQTL is excluded */ { return (eqtl->expScores[i] == 0.0); } static boolean eqtlIncludeFilter(struct track *track, void *item) /* Apply all filters (except gene) to eQTL item. Invoked by filterTissues method */ { int i; int excluded = 0; double maxEffect = 0.0; double maxProb = 0.0; struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData; for (i=0; i<eqtl->expCount; i++) { if (hashFindVal(extras->tissueHash, eqtl->expNames[i])) { - maxEffect = fmax(maxEffect, fabs(eqtl->expScores[i])); - maxProb = fmax(maxProb, fabs(eqtl->expProbs[i])); + double effect = eqtl->expScores[i]; + double prob = eqtl->expProbs[i]; + maxEffect = fmax(maxEffect, fabs(effect)); + maxProb = fmax(maxProb, fabs(prob)); + if (effect < extras->minEffect || prob < extras->minProb) + { + eqtlExcludeTissue(eqtl, i); + excluded++; + } } else { eqtlExcludeTissue(eqtl, i); excluded++; } } // exclude if no tissues match selector if (excluded == eqtl->expCount || // or if variant has no selected tissue where effect size is above cutoff maxEffect < extras->minEffect || // or if variant has no selected tissue where probability is above cutoff maxProb < extras->minProb) return FALSE; return TRUE; } static int eqtlTissueCount(struct gtexEqtlCluster *eqtl) /* Return count of non-excluded tissues in the item */ { int included = 0; int i; for (i=0; i<eqtl->expCount; i++) if (!eqtlIsExcludedTissue(eqtl, i)) included++; return included; } static int eqtlTissueIndex(struct gtexEqtlCluster *eqtl) /* Return index of first non-excluded tissue in an eQTL cluster. Used for single-tissue items. */ { int i; for (i=0; i<eqtl->expCount; i++) if (!eqtlIsExcludedTissue(eqtl, i)) return i; return -1; } static struct rgbColor eqtlTissueColor(struct track *track, struct gtexEqtlCluster *eqtl) /* Return tissue color for single-tissue item, or NULL if none found */ { int i = eqtlTissueIndex(eqtl); assert(i>=0); struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData; struct gtexTissue *tis = (struct gtexTissue *)hashFindVal(extras->tissueHash, eqtl->expNames[i]); assert (tis); return (struct rgbColor){.r=COLOR_32_BLUE(tis->color), .g=COLOR_32_GREEN(tis->color), .b=COLOR_32_RED(tis->color)}; } static char *eqtlSourcesLabel(struct gtexEqtlCluster *eqtl) /* Right label is tissue (or number of tissues if >1) */ { int ct = eqtlTissueCount(eqtl); if (ct == 1) { int i = eqtlTissueIndex(eqtl); if (i<0) errAbort("GTEx eQTL %s/%s track tissue index is negative", eqtl->name, eqtl->target); return eqtl->expNames[i]; } struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "%d tissues", ct); return dyStringCannibalize(&ds); } /* Track methods */ static void gtexEqtlClusterLoadItems(struct track *track) /* Load items in window and prune those that don't pass filter */ { /* initialize track info */ struct gtexEqtlClusterTrack *extras; AllocVar(extras); track->extraUiData = extras; char cartVar[64]; // UI settings safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_TISSUE_COLOR); extras->doTissueColor = cartUsualBoolean(cart, cartVar, GTEX_EQTL_TISSUE_COLOR_DEFAULT); boolean isFiltered = FALSE; // filter by gene via SQL safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_GENE); char *gene = cartNonemptyString(cart, cartVar); char *where = NULL; if (gene) { struct dyString *ds = dyStringNew(0); sqlDyStringPrintfFrag(ds, "%s = '%s'", GTEX_EQTL_GENE_FIELD, gene); where = dyStringCannibalize(&ds); isFiltered = TRUE; } bedLoadItemWhere(track, track->table, where, (ItemLoader)loadOne); // more filtering safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_EFFECT); extras->minEffect = fabs(cartUsualDouble(cart, cartVar, GTEX_EQTL_EFFECT_DEFAULT)); safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_PROBABILITY); extras->minProb = cartUsualDouble(cart, cartVar, GTEX_EQTL_PROBABILITY_DEFAULT); boolean hasTissueFilter = filterTissuesFromCart(track, extras); if (hasTissueFilter || extras->minEffect != 0.0 || extras->minProb != 0.0) { isFiltered = TRUE; filterItems(track, eqtlIncludeFilter, "include"); } if (isFiltered) labelTrackAsFiltered(track); } static char *gtexEqtlClusterItemName(struct track *track, void *item) /* Left label is gene name */ { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; return eqtl->target; } // blues #define EQTL_COLOR_HIGH_NEGATIVE MAKECOLOR_32(0x0, 0x0, 0xff) #define EQTL_COLOR_LOW_NEGATIVE MAKECOLOR_32(0xa0, 0xa0, 0xff) // reds #define EQTL_COLOR_HIGH_POSITIVE MAKECOLOR_32(0xff, 0x0, 0x0) #define EQTL_COLOR_LOW_POSITIVE MAKECOLOR_32(0xff, 0xa0, 0xa0) // gray #define EQTL_COLOR_MIXED MAKECOLOR_32(0x69, 0x69, 0x69) static Color gtexEqtlClusterItemColor(struct track *track, void *item, struct hvGfx *hvg) /* Color by highest effect in list (blue -, red +), grayed for lower effect. Gray if mixed effect*/ { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; double maxEffect = 0.0; double minEffect = 0.0; int i; for (i=0; i<eqtl->expCount; i++) { if (eqtlIsExcludedTissue(eqtl, i)) continue; double effect = eqtl->expScores[i]; if (effect > maxEffect) maxEffect = effect; else if (effect < minEffect) minEffect = effect; } if (minEffect < 0.0 && maxEffect > 0.0) // mixed effect return EQTL_COLOR_MIXED; double cutoff = 2.0; if (minEffect < 0.0) { // down-regulation displayed as blue if (minEffect < 0.0 - cutoff) return EQTL_COLOR_HIGH_NEGATIVE; return EQTL_COLOR_LOW_NEGATIVE; } // up-regulation displayed as red if (maxEffect > cutoff) return EQTL_COLOR_HIGH_POSITIVE; return EQTL_COLOR_LOW_POSITIVE; } /* Helper macros */ #define tissueColorPatchSpacer (max(2, tl.nWidth/4)) #define tissueColorPatchWidth (tl.nWidth * .8) static int gtexEqtlClusterItemRightPixels(struct track *track, void *item) /* Return number of pixels we need to the right of an item (for sources label). */ { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; int ret = mgFontStringWidth(tl.font, eqtlSourcesLabel(eqtl)); if (eqtlTissueCount(eqtl) == 1) ret += tissueColorPatchWidth + tissueColorPatchSpacer; return ret; } static void gtexEqtlClusterDrawItemAt(struct track *track, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw GTEx eQTL cluster with right label indicating source(s) */ { bedDrawSimpleAt(track, item, hvg, xOff, y, scale, font, color, vis); if (vis != tvFull && vis != tvPack) return; /* Draw text to the right */ struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData; int x2 = round((double)((int)eqtl->chromEnd-winStart)*scale) + xOff; int x = x2 + tl.mWidth/2; char *label = eqtlSourcesLabel(eqtl); int w = mgFontStringWidth(font, label); hvGfxTextCentered(hvg, x, y, w, track->heightPer, MG_BLACK, font, label); if (eqtlTissueCount(eqtl) == 1 && extras->doTissueColor) { // tissue color patch (box) x += w; int h = w = tissueColorPatchWidth; struct rgbColor tisColor = eqtlTissueColor(track, eqtl); int ix = hvGfxFindColorIx(hvg, tisColor.r, tisColor.g, tisColor.b); hvGfxBox(hvg, x + tissueColorPatchSpacer, y + (tl.fontHeight - h)/2 + tl.fontHeight/10, w, h, ix); } } static void gtexEqtlClusterMapItem(struct track *track, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) /* Create a map box on item and label with list of tissues with colors and effect size */ { char *title = itemName; if (track->limitedVis != tvDense) { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "%s/%s: ", eqtl->name, eqtl->target); int i; for (i=0; i<eqtl->expCount; i++) { if (eqtlIsExcludedTissue(eqtl, i)) continue; double effect= eqtl->expScores[i]; dyStringPrintf(ds, "%s(%s%0.2f)%s", eqtl->expNames[i], effect < 0 ? "" : "+", effect, i < eqtl->expCount - 1 ? ", " : ""); } title = dyStringCannibalize(&ds); } int w = width + gtexEqtlClusterItemRightPixels(track, item); genericMapItem(track, hvg, item, title, itemName, start, end, x, y, w, height); } void gtexEqtlClusterMethods(struct track *track) /* BED5+5 with target, expNames,expScores, expProbs */ { track->loadItems = gtexEqtlClusterLoadItems; track->itemName = gtexEqtlClusterItemName; track->itemColor = gtexEqtlClusterItemColor; track->itemRightPixels = gtexEqtlClusterItemRightPixels; track->drawItemAt = gtexEqtlClusterDrawItemAt; track->mapItem = gtexEqtlClusterMapItem; }