7b7d273fd3aeee222d5ee8540298ac6dee662605 kate Wed Sep 13 11:45:23 2017 -0700 Add UI setting to toggle display of tissue color patches (for single-tissue eQTL's. It can be distracting in large regions. refs #15646 diff --git src/hg/inc/gtexUi.h src/hg/inc/gtexUi.h index 52caca4..b68c35a 100644 --- src/hg/inc/gtexUi.h +++ src/hg/inc/gtexUi.h @@ -1,140 +1,145 @@ /* gtexUi - GTEx (Genotype Tissue Expression) tracks */ /* Copyright (C) 2015 The Regents of the University of California * See README in this or parent directory for licensing information. */ #ifndef GTEXUI_H #define GTEXUI_H /* Color scheme */ #define GTEX_COLORS "colorScheme" #define GTEX_COLORS_RAINBOW "rainbow" /* Color scheme from GTEX papers and portal */ #define GTEX_COLORS_GTEX "gtex" #define GTEX_COLORS_DEFAULT GTEX_COLORS_GTEX /* Data transform */ // WARNING: this also appears in JS #define GTEX_LOG_TRANSFORM "logTransform" #define GTEX_LOG_TRANSFORM_DEFAULT TRUE /* Viewing limits */ // WARNING: this also appears in JS #define GTEX_MAX_VIEW_LIMIT "maxViewLimit" #define GTEX_MAX_VIEW_LIMIT_DEFAULT 300 /* TODO: Get default from gtexInfo table */ /* Sample selection and comparison */ // WARNING: this also appears in JS #define GTEX_SAMPLES "samples" #define GTEX_SAMPLES_ALL "all" #define GTEX_SAMPLES_COMPARE_SEX "sex" #define GTEX_SAMPLES_DEFAULT GTEX_SAMPLES_ALL #define GTEX_SAMPLES_COMPARE_AGE "age" #define GTEX_COMPARE_AGE_YEARS "years" #define GTEX_COMPARE_AGE_DEFAULT 50 // WARNING: this also appears in JS #define GTEX_COMPARISON_DISPLAY "comparison" #define GTEX_COMPARISON_MIRROR "mirror" #define GTEX_COMPARISON_DIFF "difference" #define GTEX_COMPARISON_DEFAULT GTEX_COMPARISON_DIFF /* Graph type */ #define GTEX_GRAPH "graphType" #define GTEX_GRAPH_RAW "raw" #define GTEX_GRAPH_NORMAL "normalized" #define GTEX_GRAPH_DEFAULT GTEX_GRAPH_RAW /* Tissue filter */ #define GTEX_TISSUE_SELECT "tissues" /* Gene filter */ #define GTEX_CODING_GENE_FILTER "codingOnly" #define GTEX_CODING_GENE_FILTER_DEFAULT FALSE /* Hide exons */ #define GTEX_SHOW_EXONS "showExons" #define GTEX_SHOW_EXONS_DEFAULT FALSE /* Suppress whiteout behind graph (to show highlight and blue lines) */ #define GTEX_NO_WHITEOUT "noWhiteout" #define GTEX_NO_WHITEOUT_DEFAULT FALSE /* Item name is gene symbol, accession, or both */ #define GTEX_LABEL "label" #define GTEX_LABEL_SYMBOL "name" #define GTEX_LABEL_ACCESSION "accession" #define GTEX_LABEL_BOTH "both" #define GTEX_LABEL_DEFAULT GTEX_LABEL_SYMBOL /* GTEx eQTL track controls */ #define GTEX_EQTL_EFFECT "effect" #define GTEX_EQTL_PROBABILITY "prob" #define GTEX_EQTL_PROBABILITY_DEFAULT 0.0 #define GTEX_EQTL_GENE "gene" +#define GTEX_EQTL_TISSUE_COLOR "tissueColor" +#define GTEX_EQTL_TISSUE_COLOR_DEFAULT TRUE /* Identify GTEx tracks that use special trackUI. * NOTE: trackDb must follow this naming convention unless/until there is * a new trackType. */ #define GTEX_GENE_TRACK_BASENAME "gtexGene" #define GTEX_EQTL_TRACK_BASENAME "gtexEqtlCluster" boolean gtexIsGeneTrack(char *trackName); /* Identify GTEx gene track so custom trackUi CGI can be launched */ boolean gtexIsEqtlTrack(char *trackName); /* Identify GTEx eqtl track so custom trackUi CGI can be launched */ char *gtexTrackUiName(); /* Refer to Body Map CGI if suitable */ void gtexPortalLink(char *geneId); /* print URL to GTEX portal gene expression page using Ensembl Gene Id*/ 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 */ /* UI controls */ void gtexGeneUiGeneLabel(struct cart *cart, char *track, struct trackDb *tdb); /* Radio buttons to select format of gene label */ void gtexGeneUiCodingFilter(struct cart *cart, char *track, struct trackDb *tdb); /* Checkbox to restrict display to protein coding genes */ void gtexGeneUiGeneModel(struct cart *cart, char *track, struct trackDb *tdb); /* Checkbox to enable display of GTEx gene model */ void gtexGeneUiLogTransform(struct cart *cart, char *track, struct trackDb *tdb); /* Checkbox to select log-transformed RPKM values */ void gtexGeneUiViewLimits(struct cart *cart, char *track, struct trackDb *tdb); /* Set viewing limits if log transform not checked */ void gtexGeneUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* GTEx (Genotype Tissue Expression) per gene data */ -void gtexEqtlGene(struct cart *cart, char *track, struct trackDb *tdb); +void gtexEqtlUiGene(struct cart *cart, char *track, struct trackDb *tdb); /* Limit to selected gene */ -void gtexEqtlEffectSize(struct cart *cart, char *track, struct trackDb *tdb); +void gtexEqtlUiEffectSize(struct cart *cart, char *track, struct trackDb *tdb); /* Limit to items with absolute value of effect size >= threshold. Use largest * effect size in tissue list */ -void gtexEqtlProbability(struct cart *cart, char *track, struct trackDb *tdb); +void gtexEqtlUiProbability(struct cart *cart, char *track, struct trackDb *tdb); /* Limit to items with specified probability. Use largest probability in tissue list, * which is score/1000, so use that */ +void gtexEqtlUiTissueColor(struct cart *cart, char *track, struct trackDb *tdb); +/* Control visibility color patch to indicate tissue (can be distracting in large regions) */ + void gtexEqtlClusterUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed); /* GTEx (Genotype Tissue Expression) eQTL clusters. Use this on right-click, * (when hgGtexTrackSettings can't be) */ #endif /* GTEXUI_H */