9f48c12faa3df72b9ab3e6455095ee897c646532
kate
  Tue Oct 20 21:56:56 2015 -0700
Scale graph limits and place X axis labels appropriately for variously ranged graphs, and log transformed data. refs #15645

diff --git src/hg/hgc/gtexClick.c src/hg/hgc/gtexClick.c
index 5734f12..5195750 100644
--- src/hg/hgc/gtexClick.c
+++ src/hg/hgc/gtexClick.c
@@ -62,39 +62,41 @@
 int i;
 int sampleId=1;
 for (tsv = tsvList; tsv != NULL; tsv = tsv->next)
     {
     int count = tsv->count;
     for (i=0; i<count; i++)
         fprintf(f, "%d\t%s\t%0.3f\n", sampleId++, tsv->name, tsv->vals[i]);
     }
 fclose(f);
 
 // Plot to PNG file
 struct tempName pngTn;
 trashDirFile(&pngTn, "hgc", "gtexGene", ".png");
 char cmd[256];
 // Exec R in quiet mode, without reading/saving environment or workspace
-safef(cmd, sizeof(cmd), "Rscript --gui=X11 --vanilla --slave gtex/geneBoxplot.R %s %s %s",  
-                                gtexGene->name, dfTn.forCgi, pngTn.forHtml);
+//safef(cmd, sizeof(cmd), "Rscript --gui=X11 --vanilla --slave gtex/geneBoxplot.R %s %s %s",  
+safef(cmd, sizeof(cmd), "Rscript --vanilla --slave gtex/geneBoxplot.R %s %s %s %s",  
+                                gtexGene->name, dfTn.forCgi, pngTn.forHtml, 
+                                doLogTransform ? "log=TRUE" : "log=FALSE");
 int ret = system(cmd);
 if (ret == 0)
     {
-    //printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml);
-    printf("<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
+    printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml);
+    //printf("<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
                     //pngTn.forHtml, imageWidth, imageHeight);
-                    pngTn.forHtml, 900, 500);
+                    //pngTn.forHtml, 900, 500);
     }
 }
 
 void d3GtexBoxplot(struct tissueSampleVals *tsvList)
 {
 //puts("<script src='http://www.d3plus.org/js/d3.js'></script>\n");
 //puts("<script src='http://www.d3plus.org/js/d3plus.js'></script>\n");
 printf("<div id='expGraph'></div>\n");
 jsIncludeFile("d3.min.js", NULL);
 jsIncludeFile("d3plus.gtex.js", NULL);
 jsTrackingVar("geneName", gtexGene->name);
 jsTrackingVar("geneId", gtexGene->geneId);
 jsIncludeFile("gtex.js", NULL);
 }