533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/lib/gtexBoxplot.c src/hg/lib/gtexBoxplot.c
deleted file mode 100644
index 3813f93..0000000
--- src/hg/lib/gtexBoxplot.c
+++ /dev/null
@@ -1,161 +0,0 @@
-/* Create a PNG file with boxplot of gene expression 
- *      for GTEx (Genotype Tissue Expression) data. */
-
-/* Copyright (C) 2016 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
-
-#include "common.h"
-#include "hash.h"
-#include "trashDir.h"
-#include "gtexInfo.h"
-#include "gtexTissue.h"
-#include "gtexSampleData.h"
-#include "pipeline.h"
-
-struct tissueSampleVals
-/* RPKM expression values for multiple samples */
-/* (Data structure shared by different implementations of boxplot (e.g. C, JS),
- * later abandoned) */
-    {
-    struct tissueSampleVals *next;
-    char *name;         /* GTEx tissue name */
-    char *description;  /* GTEx tissue description */
-    int color;          /* GTEx tissue color */
-    int count;          /* number of samples */
-    double *vals;       /* RPKM values */
-    double min, max;    /* minimum, maximum value */
-    double q1, median, q3;      /* quartiles */
-    struct slDouble *valList;   /* used to create val array */
-    };
-
-static struct tissueSampleVals *getTissueSampleVals(char *geneId, boolean doLogTransform,
-                                                char *version, double *maxValRet)
-/* Get sample data for the gene.  Optionally log10 it. Return maximum value seen */
-{
-struct hash *tsHash = hashNew(0);
-struct tissueSampleVals *tsv;
-struct hashEl *hel;
-struct slDouble *val;
-double maxVal = 0;
-struct gtexSampleData *sd = NULL;
-char query[256];
-char **row;
-char buf[256];
-char *sampleDataTable = "gtexSampleData";
-safef(buf, sizeof(buf), "%s%s", sampleDataTable, gtexVersionSuffixFromVersion(version));
-struct sqlConnection *conn = hAllocConn("hgFixed");
-assert(sqlTableExists(conn, buf));
-sqlSafef(query, sizeof(query), "select * from %s where geneId='%s'", buf, geneId);
-struct sqlResult *sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    sd = gtexSampleDataLoad(row);
-    if ((hel = hashLookup(tsHash, sd->tissue)) == NULL)
-        {
-        AllocVar(tsv);
-        hashAdd(tsHash, sd->tissue, tsv);
-        }
-    else
-        tsv = (struct tissueSampleVals *)hel->val;
-    maxVal = max(maxVal, sd->score);
-    val = slDoubleNew(sd->score);
-    slAddHead(&tsv->valList, val);
-    }
-/*  Fill in tissue descriptions, fill values array and calculate stats for plotting
-        Then make a list, suitable for sorting by tissue or score
-    NOTE: Most of this not needed for R implementation */
-struct gtexTissue *tis = NULL, *tissues = gtexGetTissues(version);
-struct tissueSampleVals *tsList = NULL;
-int i;
-if (doLogTransform)
-    maxVal = log10(maxVal+1.0);
-for (tis = tissues; tis != NULL; tis = tis->next)
-    {
-    tsv = hashFindVal(tsHash, tis->name);
-    if (tsv == NULL)
-        {
-        /* no non-zero values for this tissue/gene */
-        AllocVar(tsv);
-        val = slDoubleNew(0.0);
-        slAddHead(&tsv->valList, val);
-        }
-    tsv->name = tis->name;
-    tsv->description = tis->description;
-    tsv->color = tis->color;
-    int count = tsv->count = slCount(tsv->valList);
-    double *vals = AllocArray(tsv->vals, count);
-    for (i=0; i<count; i++)
-        {
-        val = slPopHead(&tsv->valList);
-        if (doLogTransform)
-            vals[i] = log10(val->val+1.0);
-        else
-            vals[i] = val->val;
-        }
-    doubleBoxWhiskerCalc(tsv->count, tsv->vals, 
-                                &tsv->min, &tsv->q1, &tsv->median, &tsv->q3, &tsv->max);
-    slAddHead(&tsList, tsv);
-    }
-if (maxValRet != NULL)
-    *maxValRet = maxVal;
-return tsList;
-}
-
-/********************************************************/
-/* R implementation of GTEx boxplot.  This invokes R interpreter on an R script */
-
-static boolean drawGtexRBoxplot(char *geneName, struct tissueSampleVals *tsvList,
-                        boolean doLogTransform, char *version, struct tempName *pngTn)
-/* Draw a box-and-whiskers plot from GTEx sample data, using R boxplot */
-{
-/* Create R data frame.  This is a tab-sep file, one row per sample, 
- * with columns for sample, tissue, rpkm */
-struct tempName dfTn;
-trashDirFile(&dfTn, "hgc", "gtexGene", ".df.txt");
-FILE *f = fopen(dfTn.forCgi, "w");
-if (f == NULL)
-    errAbort("can't create temp file %s", dfTn.forCgi);
-fprintf(f, "sample\ttissue\trpkm\n");
-struct tissueSampleVals *tsv;
-int sampleId=1;
-int i;
-for (tsv = tsvList; tsv != NULL; tsv = tsv->next)
-    {
-    int count = tsv->count;
-    // remove trailing parenthesized phrases as not worth label length
-    chopSuffixAt(tsv->description, '(');
-    for (i=0; i<count; i++)
-        fprintf(f, "%d\t%s\t%0.3f\n", sampleId++, tsv->description, tsv->vals[i]);
-    }
-fclose(f);
-
-// Plot to PNG file
-if (!pngTn)
-    return FALSE;
-trashDirFile(pngTn, "hgc", "gtexGene", ".png");
-
-/* Exec R in quiet mode, without reading/saving environment or workspace */
-char *pipeCmd[] = {"Rscript","--vanilla","--slave","hgcData/gtexBoxplot.R", 
-    geneName, dfTn.forCgi, pngTn->forHtml, 
-    doLogTransform ? "log=TRUE" : "log=FALSE", "order=alpha", version, NULL};
-struct pipeline *pl = pipelineOpen1(pipeCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL);
-int ret = pipelineWait(pl);
-//NOTE: use "order=score" to order bargraph by median RPKM, descending
-
-if (ret == 0)
-    return TRUE;
-return FALSE;
-}
-
-boolean gtexGeneBoxplot(char *geneId, char *geneName, char *version, 
-                                boolean doLogTransform, struct tempName *pngTn)
-/* Create a png temp file with boxplot of GTEx expression values for this gene. 
- * GeneId is the Ensembl gene ID.  GeneName is the HUGO name, used for graph title;
- * If NULL, label with the Ensembl gene ID */
-{
-struct tissueSampleVals *tsvs;
-tsvs  = getTissueSampleVals(geneId, doLogTransform, version, NULL);
-char *label = geneName ? geneName : geneId;
-return drawGtexRBoxplot(label, tsvs, doLogTransform, version, pngTn);
-}
-