c0af5f216f8ff00466f0d222cede7f491fd17d81 galt Fri Jan 20 23:09:35 2023 -0800 More fixes for stuff found by htmlCheck, refs #7914 diff --git src/hg/near/hgNear/expRatio.c src/hg/near/hgNear/expRatio.c index 9584aac..8e495bd 100644 --- src/hg/near/hgNear/expRatio.c +++ src/hg/near/hgNear/expRatio.c @@ -1,809 +1,809 @@ /* Handle expression ratio (and expMulti) type microarray data. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "obscure.h" #include "sqlList.h" #include "jksql.h" #include "cart.h" #include "hdb.h" #include "hCommon.h" #include "cheapcgi.h" #include "hgExp.h" #include "hgNear.h" static char *expCellVal(struct genePos *gp, struct sqlConnection *lookupConn, char *lookupTable, struct sqlConnection *dataConn, char *dataTable, int representativeCount, int *representatives, char *format) /* Create a comma-separated string of expression values. */ { int i; struct dyString *dy = dyStringNew(1024); int valCount; float *vals = NULL; char *result; if (hgExpLoadVals(lookupConn, dataConn, lookupTable, gp->name, dataTable, &valCount, &vals)) { for (i=0; i<representativeCount; ++i) { int ix = representatives[i]; if (ix != -1) { float val = vals[ix]; if (val < -9999) dyStringPrintf(dy, "n/a"); else dyStringPrintf(dy, format, val); dyStringAppendC(dy, ','); } } freez(&vals); } else { dyStringPrintf(dy, "n/a"); } result = cloneString(dy->string); dyStringFree(&dy); return result; } static char *expRatioCellVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Get comma separated list of values. */ { return expCellVal(gp, conn, col->table, conn, col->posTable, col->representativeCount, col->representatives, "%4.3f"); } static boolean expRatioExists(struct column *col, struct sqlConnection *conn) /* This returns true if relevant tables exist. */ { boolean tableOk = sameWord(col->table, "null") || sqlTableExists(conn, col->table); boolean posTableOk = sqlTableExists(conn, col->posTable); boolean expTableOk = sqlTableExists(conn, col->experimentTable); return tableOk && posTableOk && expTableOk; } void expRatioCellPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Print out html for expRatio cell. */ { hgExpCellPrint(col->name, gp->name, conn, col->table, conn, col->posTable, col->representativeCount, col->representatives, col->expRatioUseBlue, col->forceGrayscale, !col->forceGrayscale, col->brightness); } void expLabelPrint(struct column *col, char *subName, int representativeCount, int *representatives, char *expTable) /* Print out labels of various experiments. */ { int skipName = atoi(columnSetting(col, "skipName", "0")); char *url = colInfoUrl(col); hgExpLabelPrint(database, col->name, subName, skipName, url, representativeCount, representatives, expTable, 0); freeMem(url); } void expRatioLabelPrint(struct column *col) /* Print out labels of various experiments. */ { expLabelPrint(col, "", col->representativeCount, col->representatives, col->experimentTable); } static void expBrightnessControl(struct column *col) /* Put up brightness text box. */ { char *varName = configVarName(col, "scale"); char *val = cartUsualString(cart, varName, columnSetting(col, "brightness", "1.0")); hPrintf("brightness: "); cgiMakeTextVar(varName, val, 3); } static void expRatioConfigControls(struct column *col) /* Print out configuration column */ { hPrintf("<TD>"); expBrightnessControl(col); hPrintf("</TD>"); } void expFilterControls(struct column *col, char *subName, char *experimentTable, int representativeCount, int *representatives) /* Print out controls for advanced filter. */ { char lVarName[64]; int i; int skipName = atoi(columnSetting(col, "skipName", "0")); char *experimentType = cloneString(columnSetting(col, "experimentType", "tissue")); char **experiments = hgExpGetNames(database, experimentTable, representativeCount, representatives, skipName); hPrintf("<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=0>\n"); toUpperN(experimentType, 1); hPrintf("<TR><TH>%s</TH><TH>Minimum</TH><TH>Maximum</TH></TR>\n", experimentType); for (i=0; i<representativeCount; ++i) { int ix = representatives[i]; if (ix != -1) { hPrintf("<TR>"); hPrintf("<TD> %s</TD>", experiments[i]); safef(lVarName, sizeof(lVarName), "%smin%d", subName, ix); hPrintf("<TD>"); advFilterRemakeTextVar(col, lVarName, 8); hPrintf("</TD>"); safef(lVarName, sizeof(lVarName), "%smax%d", subName, ix); hPrintf("<TD>"); advFilterRemakeTextVar(col, lVarName, 8); hPrintf("</TD>"); hPrintf("</TR>\n"); } } hPrintf("</TABLE>\n"); hPrintf("Include if "); advFilterAnyAllMenu(col, "logic", FALSE); toLowerN(experimentType, 1); hPrintf(" %ss meet minimum/maximum criteria.", experimentType); freeMem(experimentType); } static void explainLogTwoRatio(char *maxVal, char *experimentType) /* Put up note on log base 2 expression values. */ { hPrintf("Note: the values here range from about -%s to %s.<BR>\n", maxVal, maxVal); hPrintf("These are calculated as logBase2(%s/reference).<BR>\n", experimentType); } void expRatioFilterControls(struct column *col, struct sqlConnection *conn) /* Print out controls for advanced filter. */ { char *maxVal = columnSetting(col, "max", "3.0"); char *experimentType = columnSetting(col, "experimentType", "tissue"); explainLogTwoRatio(maxVal, experimentType); expFilterControls(col, "", col->experimentTable, col->representativeCount, col->representatives); } static struct hash *expValHash(struct sqlConnection *conn, char *table) /* Load up all expresssion data into a hash keyed by table->name */ { char query[256]; struct sqlResult *sr; char **row; struct hash *hash = newHash(16); sqlSafef(query, sizeof(query), "select name,expScores from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name = row[0]; if (!hashLookup(hash, name)) { float *vals = NULL; int valCount; sqlFloatDynamicArray(row[1], &vals, &valCount); hashAdd(hash, name, vals); } } sqlFreeResult(&sr); return hash; } struct hash *getNameExpHash(struct sqlConnection *conn, char *table, char *keyField, char *valField, struct hash *expHash) /* For each key in table lookup val in expHash, and if there * put key/exp in table. */ { char query[256]; struct sqlResult *sr; char **row; struct hash *hash = newHash(16); sqlSafef(query, sizeof(query), "select %s,%s from %s", keyField, valField,table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { float *val = hashFindVal(expHash, row[1]); if (val != NULL) hashAdd(hash, row[0], val); } sqlFreeResult(&sr); return hash; } static char *expLimitString(struct column *col, char *subName, int *representatives, int repIx, boolean isMax) /* Return string value of min/max variable for a given expression * experiment. */ { char varName[64]; static char *varType[2] = {"min", "max"}; safef(varName, sizeof(varName), "%s%s%d", subName, varType[isMax], representatives[repIx]); return advFilterVal(col, varName); } static boolean expAdvFilterUsed(struct column *col, char *subName) /* Return TRUE if any of the advanced filter variables * for this col are set. */ { char wild[128]; safef(wild, sizeof(wild), "%s%s.%s*", advFilterPrefix, col->name, subName); return anyRealInCart(cart, wild); } struct genePos *expAdvFilter(struct column *col, char *subName, struct sqlConnection *lookupConn, char *lookupTable, struct sqlConnection *dataConn, char *dataTable, int representativeCount, int *representatives, struct genePos *list) /* Do advanced filter on position. */ { if (expAdvFilterUsed(col, subName)) { struct hash *expHash = expValHash(dataConn, dataTable); struct hash *nameExpHash = sameWord(lookupTable,"null") ? expHash : getNameExpHash(lookupConn, lookupTable, "name", "value", expHash); boolean orLogic = advFilterOrLogic(col, "logic", FALSE); int isMax; int repIx; char *varValString; char **mms[2]; /* Min/max strings. */ float *mmv[2]; /* Min/max values. */ struct genePos *newList = NULL, *gp, *next; /* Fetch all limit variables. */ for (isMax=0; isMax<2; ++isMax) { AllocArray(mms[isMax], representativeCount); AllocArray(mmv[isMax], representativeCount); for (repIx=0; repIx < representativeCount; ++repIx) { varValString = mms[isMax][repIx] = expLimitString(col, subName, representatives, repIx, isMax); if (varValString != NULL) { mmv[isMax][repIx] = atof(varValString); } } } /* Step through each item in list and figure out if it is in. */ for (gp = list; gp != NULL; gp = next) { float *vals; next = gp->next; if ((vals = hashFindVal(nameExpHash, gp->name)) != NULL) { boolean passes = !orLogic; for (repIx=0; repIx<representativeCount; ++repIx) { boolean anyLimit = FALSE; boolean passesOne = TRUE; float val = vals[representatives[repIx]]; for (isMax=0; isMax<2; ++isMax) { if (mms[isMax][repIx] != NULL) { float varVal = mmv[isMax][repIx]; anyLimit = TRUE; if (isMax) { if (val > varVal) passesOne = FALSE; } else { if (val < varVal) passesOne = FALSE; } } } if (anyLimit) { if (orLogic) { passes |= passesOne; } else { passes &= passesOne; } } } if (passes) { slAddHead(&newList, gp); } } } slReverse(&newList); list = newList; /* cleanup . */ for (isMax=0; isMax<2; ++isMax) { freez(&mms[isMax]); freez(&mmv[isMax]); } freeHash(&nameExpHash); freeHashAndVals(&expHash); } return list; } struct genePos *expRatioAdvFilter(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced filter on position. */ { return expAdvFilter(col, "", conn, col->table, conn, col->posTable, col->representativeCount, col->representatives, list); } int expRatioTableColumns(struct column *col) /* Return number of html columns this uses. */ { int *reps = col->representatives; int repCount = col->representativeCount; int i, count = 1; for (i=0; i<repCount; ++i) if (reps[i] == -1) ++count; return count; } void setupColumnExpRatio(struct column *col, char *parameters) /* Set up expression ratio type column. */ { /* Hash up name value pairs and extract some we care about. */ char *repList = columnSetting(col, "representatives", NULL); char *expMax = columnSetting(col, "max", "3.0"); col->table = cloneString(nextWord(¶meters)); col->posTable = cloneString(nextWord(¶meters)); col->experimentTable = cloneString(nextWord(¶meters)); if (col->posTable == NULL) errAbort("missing parameters from type line of %s", col->name); /* Convert list of ascii number in repList to an array of binary * numbers in col->representatives. */ if (repList != NULL) { char *dupe = cloneString(repList); sqlSignedDynamicArray(dupe, &col->representatives, &col->representativeCount); freez(&dupe); } else { errAbort("Missing required representatives list in %s", col->name); } /* Figure out color scheme. */ { char *forceGrayscale = columnSetting(col, "forceGrayscale", "off"); col->forceGrayscale = (sameWord(forceGrayscale,"on")) ? TRUE : FALSE; col->expRatioUseBlue = hgExpRatioUseBlue(cart, expRatioColorVarName); } /* Figure out scale. */ { char *varName = configVarName(col, "scale"); char *val = cartUsualString(cart, varName, "1"); char *raVal = columnSetting(col, "brightness", "1"); double fVal = (cartVarExists(cart, varName)) ? atof(val) : atof(raVal); if (fVal == 0) fVal = 1.0; col->brightness = fVal/atof(expMax); } col->exists = expRatioExists; col->cellVal = expRatioCellVal; col->cellPrint = expRatioCellPrint; col->labelPrint = expRatioLabelPrint; col->configControls = expRatioConfigControls; col->filterControls = expRatioFilterControls; col->advFilter = expRatioAdvFilter; } /* --------- expMulti stuff for more complex expression ratio tracks -------- */ static struct expMultiData *emdNew(char *name, char *label, char *spec) /* Create new expMultiData based on spec. */ { char *dupe = cloneString(spec); char *s = dupe; char *repString; struct expMultiData *emd; AllocVar(emd); emd->name = cloneString(name); emd->shortLabel = cloneString(label); emd->experimentTable = cloneString(nextWord(&s)); emd->ratioTable = cloneString(nextWord(&s)); emd->absoluteTable = cloneString(nextWord(&s)); repString = nextWord(&s); if (repString == NULL) errAbort("Short spec in emdNew"); sqlSignedDynamicArray(repString, &emd->representatives, &emd->representativeCount); freeMem(dupe); return emd; } static struct expMultiData *makeEmd(struct column *col, char *name, char *label, struct expMultiData **pList) /* Create new expMultiData based on specs in column settings and hang it on list. */ { char *spec = hashFindVal(col->settings, name); struct expMultiData *emd; if (spec == NULL) return NULL; emd = emdNew(name, label, spec); slAddHead(pList, emd); return emd; } struct expMultiData *emdFind(struct expMultiData *list, char *name) /* Find named expMultiData, or NULL if not on list. */ { struct expMultiData *emd; for (emd = list; emd != NULL; emd = emd->next) if (sameString(name, emd->name)) return emd; return NULL; } struct expMultiData *getSelectedEmd(struct column *col, struct expMultiData *emdList) /* Get user selected column or default. */ { struct expMultiData *emd = NULL; char *emdVal = configVarVal(col, "emd"); if (emdVal != NULL) emd = emdFind(emdList, emdVal); if (emd == NULL) emd = emdList; return emd; } static boolean expMultiExists(struct column *col, struct sqlConnection *conn) /* Returns true if relevant tables exist. */ { struct sqlConnection *fConn = hgFixedConn(); struct expMultiData *emd; if (!sqlTableExists(conn, col->table)) return FALSE; for (emd = col->emdList; emd != NULL; emd = emd->next) { if (!sqlTableExists(fConn, emd->ratioTable)) return FALSE; if (!sqlTableExists(fConn, emd->absoluteTable)) return FALSE; } return TRUE; } static char *expMultiCellVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Return comma separated string. */ { struct expMultiData *emd = col->emd; char *dataTable; char *format; char *ret; if (col->expShowAbs) { dataTable = emd->absoluteTable; format = "%2.1f"; } else { dataTable = emd->ratioTable; format = "%4.3f"; } ret = expCellVal(gp, conn, col->table, hgFixedConn(), dataTable, emd->representativeCount, emd->representatives, format); return ret; } void expMultiCellPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Print out html for expMulti cell. */ { struct expMultiData *emd = col->emd; char *dataTable; float scale; if (col->expShowAbs) { dataTable = emd->absoluteTable; scale = col->expAbsScale; } else { dataTable = emd->ratioTable; scale = col->expRatioScale; } hgExpCellPrint(col->name, gp->name, conn, col->table, hgFixedConn(), dataTable, emd->representativeCount, emd->representatives, col->expRatioUseBlue, col->expShowAbs, TRUE, scale); } void expMultiLabelPrint(struct column *col) /* Print out labels of various experiments. */ { struct expMultiData *emd = col->emd; expLabelPrint(col, emd->name, emd->representativeCount, emd->representatives, emd->experimentTable); } static void expEmdControl(struct column *col) /* Show selected/median/all control. */ { struct expMultiData *emd; struct expMultiData *curEmd = getSelectedEmd(col, col->emdList); char *experimentType = columnSetting(col, "experimentType", "tissue"); hPrintf("%ss: ", experimentType); hPrintf("<SELECT NAME=\"%s\">", configVarName(col, "emd")); for (emd = col->emdList; emd != NULL; emd = emd->next) { hPrintf("<OPTION VALUE=\"%s\"", emd->name); if (emd == curEmd) hPrintf(" SELECTED"); - hPrintf(">%s", emd->shortLabel); + hPrintf(">%s</OPTION>", emd->shortLabel); } hPrintf("</SELECT>\n"); } static void expAbsRatioControl(struct column *col) /* Show ratio/absolute control. */ { char *name = configVarName(col, "ratioAbs"); char *curVal = cartUsualString(cart, name, "ratio"); static char *choices[2] = {"ratio", "absolute"}; hPrintf("values: "); cgiMakeDropList(name, choices, ArraySize(choices), curVal); } static void expMultiConfigControls(struct column *col) /* Print out configuration column */ { hPrintf("<TD>"); hPrintf("<TABLE><TR><TD>"); expBrightnessControl(col); hPrintf("</TD><TD>"); expEmdControl(col); hPrintf("</TD><TD>"); expAbsRatioControl(col); hPrintf("</TD></TR></TABLE>"); hPrintf("</TD>"); } static void expMultiFilterPrefix(struct column *col, int maxPrefixSize, char *retPrefix ) /* Fill in prefix to use for filter variables in this multi configuration. */ { char *absRel = (col->expShowAbs ? "abs" : "rel"); safef(retPrefix, maxPrefixSize, "%s.%s.", absRel, col->emd->name); } static void explainAbsolute(char *maxVal) /* Explain a little about absolutes. */ { hPrintf("Note: the values here range up to about %s.<BR>\n", maxVal); hPrintf("Values of 20 or less indicate unmeasurable expression.<BR>\n"); } static void expMultiFilterControls(struct column *col, struct sqlConnection *conn) /* Print out controls for advanced filter. */ { char emfPrefix[64]; struct expMultiData *emd = col->emd; if (col->expShowAbs) { char *absoluteMax = columnSetting(col, "absoluteMax", "30000"); explainAbsolute(absoluteMax); } else { char *ratioMax = columnSetting(col, "ratioMax", "3.0"); char *experimentType = columnSetting(col, "experimentType", "tissue"); explainLogTwoRatio(ratioMax, experimentType); } expMultiFilterPrefix(col, sizeof(emfPrefix), emfPrefix); expFilterControls(col, emfPrefix, emd->experimentTable, emd->representativeCount, emd->representatives); hPrintf("<BR>Other filter controls for this %s column will be<BR>", col->shortLabel); hPrintf("displayed if the column is configured differently. Only<BR>"); hPrintf("the displayed controls are active."); } struct genePos *expMultiAdvFilter(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced filter on position. */ { char *dataTable; char emfPrefix[64]; struct expMultiData *emd = col->emd; if (col->expShowAbs) dataTable = emd->absoluteTable; else dataTable = emd->ratioTable; expMultiFilterPrefix(col, sizeof(emfPrefix), emfPrefix); return expAdvFilter(col, emfPrefix, conn, col->table, hgFixedConn(), dataTable, emd->representativeCount, emd->representatives, list); } void setupColumnExpMulti(struct column *col, char *parameters) /* Set up expression type column that can be ratio or absolute, * short or long. */ { struct expMultiData *emdList = NULL; char *ratioMax = columnSetting(col, "ratioMax", "3.0"); char *absoluteMax = columnSetting(col, "absoluteMax", "30000"); col->table = cloneString(nextWord(¶meters)); if (col->table == NULL) errAbort("missing parameters from type line of %s", col->name); /* Check that we have at least one set of experiments to display, * and set the current experiments. */ makeEmd(col, "all", "all replicates", &emdList); // customize otherwise confusing menu option for GTEx. Simply, this option selects all tissues. makeEmd(col, "median", startsWith("gtex", col->name) ? "all" : "median of replicates", &emdList); makeEmd(col, "selected", "selected", &emdList); if (emdList == NULL) errAbort("Need at least one of all/median/selected for %s", col->name); col->emdList = emdList; col->emd = getSelectedEmd(col, emdList); /* Figure out whether showing absolute or relative */ { char *val = cartUsualString(cart, configVarName(col, "ratioAbs"), "ratio"); col->expShowAbs = sameString(val, "absolute"); } /* Figure out color scheme. */ { col->expRatioUseBlue = hgExpRatioUseBlue(cart, expRatioColorVarName); } /* Figure out scale. */ { char *varName = configVarName(col, "scale"); char *val = cartUsualString(cart, varName, "1"); double fVal = atof(val); if (fVal == 0) fVal = 1.0; col->expRatioScale = fVal/atof(ratioMax); col->expAbsScale = fVal/log(atof(absoluteMax)); } col->exists = expMultiExists; col->configControls = expMultiConfigControls; col->cellVal = expMultiCellVal; col->cellPrint = expMultiCellPrint; col->labelPrint = expMultiLabelPrint; col->filterControls = expMultiFilterControls; col->advFilter = expMultiAdvFilter; } /* --------- expMax stuff to show maximum expression value -------- */ boolean expMaxExists(struct column *col, struct sqlConnection *conn) /* This returns true if col->table exists. */ { return sqlTableExists(conn, col->table) && sqlTableExists(hgFixedConn(), col->posTable); } static float expMaxVal(struct column *col, struct genePos *gp, struct sqlConnection *conn, struct sqlConnection *fConn) /* Return maximum expression value or -10000 if there's a problem. */ { char query[256]; char expName[64]; float maxVal = -10000; boolean noLookup = sameWord(col->table, "null"); if (!noLookup) sqlSafef(query, sizeof(query), "select value from %s where name = '%s'", col->table, gp->name); if (noLookup || (sqlQuickQuery(conn, query, expName, sizeof(expName)) != NULL)) { char *commaString = NULL; sqlSafef(query, sizeof(query), "select expScores from %s where name = '%s'", col->posTable, (noLookup) ? gp->name : expName); if ((commaString = sqlQuickString(fConn, query)) != NULL) { float *vals = NULL; int valCount, i; maxVal = atof(commaString); sqlFloatDynamicArray(commaString, &vals, &valCount); for (i=1; i<valCount; ++i) if (maxVal < vals[i]) maxVal = vals[i]; freeMem(commaString); freeMem(vals); } } return maxVal; } static char *expMaxCellVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Return value as string for this cell. */ { float maxVal = expMaxVal(col, gp, conn, hgFixedConn()); char buf[32]; if (maxVal <= -10000) return NULL; safef(buf, sizeof(buf), "%1.1f", maxVal); return cloneString(buf); } struct genePos *expMaxAdvFilter(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced filter on max expression. */ { char *minString = advFilterVal(col, "min"); char *maxString = advFilterVal(col, "max"); if (minString != NULL || maxString != NULL) { struct sqlConnection *fConn = hgFixedConn(); struct genePos *passList = NULL, *gp, *next; float minVal = 0, maxVal = 0, val; if (minString != NULL) minVal = atof(minString); if (maxString != NULL) maxVal = atof(maxString); for (gp = list; gp != NULL; gp = next) { next = gp->next; val = expMaxVal(col, gp, conn, fConn); if (minString != NULL && val < minVal) continue; if (maxString != NULL && val > maxVal) continue; slAddHead(&passList, gp); } slReverse(&passList); return passList; } else return list; } void setupColumnExpMax(struct column *col, char *parameters) /* Set up maximum expression value column. */ { col->table = cloneString(nextWord(¶meters)); col->posTable = cloneString(nextWord(¶meters)); if (col->posTable == NULL) errAbort("Not enough fields in type expMax for %s", col->name); col->exists = expMaxExists; col->cellVal = expMaxCellVal; col->filterControls = minMaxAdvFilterControls; col->advFilter = expMaxAdvFilter; }