f863c012ea39c498eaf4cff84f85f92fef210c5f jcasper Mon May 13 00:51:57 2019 -0700 Initial commit of Hi-C display support via .hic files, refs #18842 diff --git src/hg/lib/hicUi.c src/hg/lib/hicUi.c new file mode 100644 index 0000000..28133e4 --- /dev/null +++ src/hg/lib/hicUi.c @@ -0,0 +1,265 @@ +/* hic track controls */ + +/* Copyright (C) 2019 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + +#include "cheapcgi.h" +#include "cart.h" +#include "hui.h" +#include "web.h" +#include "trackDb.h" +#include "hicUi.h" +#include "Cstraw.h" +#include "regexHelper.h" +#include "obscure.h" + +char *hicUiFetchNormalization(struct cart *cart, char *track, struct hicMeta *meta) +/* Return the current normalization selection, or the default if none + * has been selected. Right now this is a hard-coded set specifically for + * .hic files, but in the future this list might be dynamically determined by + * the contents and format of the Hi-C file. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_NORMALIZATION); +char *selected = cartNonemptyString(cart, cartVar); +char *menu[] = {"NONE", "VC", "VC_SQRT", "KR"}; +int i, sanityCheck = 0; +for (i=0; i<4; i++) + { + if (sameOk(selected, menu[i])) + sanityCheck = 1; + } +if (!sanityCheck) + { + selected = menu[0]; + } +return selected; +} + +void hicUiNormalizationMenu(struct cart *cart, char *track, struct hicMeta *meta) +/* Draw a menu to select the normalization method to use. */ +{ +char cartVar[1024]; +printf("<b>Score normalization:</b> "); +char* selected = hicUiFetchNormalization(cart, track, meta); +char *menu[] = {"NONE", "VC", "VC_SQRT", "KR"}; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_NORMALIZATION); +cgiMakeDropList(cartVar, menu, 4, selected); +} + +char *hicUiFetchResolution(struct cart *cart, char *track, struct hicMeta *meta) +/* Return the current resolution selection, or the default if none + * has been selected. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_RESOLUTION); +char *selected = cartNonemptyString(cart, cartVar); +int sanityCheck = sameOk(selected, "Auto"); +int i; +for (i=0; i<meta->nRes; i++) + { + if (sameOk(selected, meta->resolutions[i])) + sanityCheck = 1; + } +if (!sanityCheck) + selected = "Auto"; +return selected; +} + +void hicUiResolutionMenu(struct cart *cart, char *track, struct hicMeta *meta) +/* Draw a menu to select which binSize to use for fetching data */ +{ +char cartVar[1024]; +char autoscale[10] = "Auto"; +printf("<b>Resolution:</b> "); +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_RESOLUTION); +char **menu = calloc(meta->nRes+1, sizeof(char*)); +char **values = calloc(meta->nRes+1, sizeof(char*)); +menu[0] = autoscale; +values[0] = autoscale; +int i; +for (i=1; i<meta->nRes+1; i++) + { + char buffer[1024]; + long long value = atoll(meta->resolutions[i-1]); + sprintWithSiBaseUnit(buffer, sizeof(buffer), value); + menu[i] = cloneString(buffer); + values[i] = cloneString(meta->resolutions[i-1]); + } +char *selected = hicUiFetchResolution(cart, track, meta); +cgiMakeDropListWithVals(cartVar, menu, values, meta->nRes+1, selected); +free(menu); +} + + +char *hicUiFetchDrawMode(struct cart *cart, char *track) +/* Return the current draw mode selection, or the default if none + * has been selected. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MODE); +char* selected = cartNonemptyString(cart, cartVar); +if ( !sameOk(selected, HIC_DRAW_MODE_SQUARE) && + !sameOk(selected, HIC_DRAW_MODE_ARC) && + !sameOk(selected, HIC_DRAW_MODE_TRIANGLE) ) + { + selected = HIC_DRAW_MODE_DEFAULT; + } +return selected; +} + + +void hicUiDrawMenu(struct cart *cart, char *track) +/* Draw the list of draw mode options for Hi-C tracks. Square is the + * standard square-shaped heatmap with the chromosome position axis on + * a diagonal from top left to bottom right. Triangle is the top half + * of that square, after rotating it 45 degrees to have the position + * axis lie horizontally. Arc draws arcs between related positions, + * but skips over self-relations. */ +{ +char cartVar[1024]; +printf("<b>Draw mode:</b> "); +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MODE); +char *menu[] = {HIC_DRAW_MODE_SQUARE, HIC_DRAW_MODE_TRIANGLE, HIC_DRAW_MODE_ARC}; +char* selected = hicUiFetchDrawMode(cart, track); +cgiMakeDropList(cartVar, menu, 3, selected); +} + + +char *hicUiFetchDrawColor(struct cart *cart, char *track) +/* Retrieve the HTML hex code for the color to draw the + * track values in (e.g., #00ffa1) */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_COLOR); +char* selected = cartNonemptyString(cart, cartVar); +if (selected == NULL) + selected = HIC_DRAW_COLOR_DEFAULT; +const char *colorExpr ="^#[0-9a-fA-F]{6}$"; +if (!regexMatch(selected, colorExpr)) + { + selected = HIC_DRAW_COLOR_DEFAULT; + } +return selected; +} + +char *hicUiFetchBgColor(struct cart *cart, char *track) +/* Retrieve the HTML hex code of the background color for the + * track. This is the color associated with scores at or close to 0. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_BG_COLOR); +char* selected = cartNonemptyString(cart, cartVar); +if (selected == NULL) + selected = HIC_DRAW_BG_COLOR_DEFAULT; +const char *colorExpr ="^#[0-9a-fA-F]{6}$"; +if (!regexMatch(selected, colorExpr)) + { + selected = HIC_DRAW_BG_COLOR_DEFAULT; + } +return selected; +} + +double hicUiFetchMaxValue(struct cart *cart, char *track) +/* Retrieve the score value at which the draw color reaches its + * its maximum intensity. Any scores above this value will + * share that same draw color. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MAX_VALUE); +return cartUsualDouble(cart, cartVar, HIC_DRAW_MAX_VALUE_DEFAULT); +} + + +void hicUiAddAutoScaleJS(struct cart *cart, char *track) +/* Write out a bit of javascript to associate checking/unchecking the autoscale + * checkbox with deactivating/activating (respectively) the maximum score + * input. */ +{ +struct dyString *new = dyStringNew(0); +dyStringPrintf(new, "$('input[name=\"%s.%s\"]')[0].onclick = function() {", track, HIC_DRAW_AUTOSCALE); +dyStringPrintf(new, "if (this.checked) {$('input[name=\"%s.%s\"]')[0].disabled = true; $('span#hicMaxText').css('color', 'gray');}", track, HIC_DRAW_MAX_VALUE); +dyStringPrintf(new, "else {$('input[name=\"%s.%s\"]')[0].disabled = false; $('span#hicMaxText').css('color', '');} };\n", track, HIC_DRAW_MAX_VALUE); +dyStringPrintf(new, "if ($('input[name=\"%s.%s\"]')[0].checked) {$('input[name=\"%s.%s\"]')[0].disabled = true; $('span#hicMaxText').css('color', 'gray');}\n", + track, HIC_DRAW_AUTOSCALE, track, HIC_DRAW_MAX_VALUE); +jsInline(dyStringContents(new)); +dyStringFree(&new); +} + +boolean hicUiFetchAutoScale(struct cart *cart, char *track) +/* Returns whether the track is configured to automatically scale its color range + * depending on the scores present in the window, or if it should stick to a + * gradient based on the user's selected maximum value. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_AUTOSCALE); +return cartUsualBoolean(cart, cartVar, TRUE); +} + + +void hicUiColorMenu(struct cart *cart, char *track) +/* Draw the menu inputs associated with selecting draw colors for the track. */ +{ +char cartVar[1024]; +printf("<b>Color:</b> "); +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_COLOR); +char* selected = hicUiFetchDrawColor(cart, track); +printf("<input type='color' name='%s' value='%s' />\n", cartVar, selected); + +// Leaving out background color options for now. We'll see if this option is requested. +/* +printf("<b>Background color:</b> "); +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_BG_COLOR); +selected = hicUiFetchBgColor(cart, track); +printf("<input type='color' name='%s' value='%s' />\n", cartVar, selected); +*/ +} + +void hicUiMaxOptionsMenu(struct cart *cart, char *track) +/* Draw the menu inputs associated with selecting whether the track should automatically + * scale its color gradient based on the scores present in the view window, or whether it + * should stick to a gradient based on a user-selected maximum score. */ +{ +char cartVar[1024]; +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MAX_VALUE); +double currentMax = hicUiFetchMaxValue(cart, track); +printf("<span id='hicMaxText'><b>Maximum:</b></span> "); +cgiMakeDoubleVar(cartVar, currentMax, 6); + +printf(" <b>Auto-scale:</b> "); +safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_AUTOSCALE); +boolean autoscaleChecked = hicUiFetchAutoScale(cart, track); +cgiMakeCheckBox(cartVar, autoscaleChecked); + +hicUiAddAutoScaleJS(cart, track); +} + +void hicCfgUi(char *database, struct cart *cart, struct trackDb *tdb, char *track, + char *title, boolean boxed) +/* Draw the list of track configuration options for Hi-C tracks */ +{ + +boxed = cfgBeginBoxAndTitle(tdb, boxed, title); +char *filename = trackDbSetting(tdb, "bigDataUrl"); +if (filename == NULL) + errAbort("Error: no bigDataUrl provided in trackDb for hic track %s", tdb->track); +struct hicMeta *trackMeta; +char *errMsg = hicLoadHeader(filename, &trackMeta); +if (errMsg != NULL) + errAbort("Error retrieving file info: %s", errMsg); + +puts("<p>"); +printf("Items are drawn in shades of the chosen color depending on score - scores above the " + "chosen maximum are drawn at full intensity.</p><p>\n"); +hicUiNormalizationMenu(cart, track, trackMeta); +puts(" "); +hicUiMaxOptionsMenu(cart, track); + +puts("</p><p>"); +hicUiDrawMenu(cart, track); +puts(" "); +hicUiResolutionMenu(cart, track, trackMeta); +puts(" "); +hicUiColorMenu(cart, track); +cfgEndBox(boxed); +}