From 0cec57ef9ada33207a6636a54276566896b21da6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 27 Aug 2019 13:08:37 -0500
Subject: Zooming on a chromosome now also zooms the genome browser
Added genome browser css because it wasn't previously committed
---
wqflask/wqflask/marker_regression/run_mapping.py | 25 ++++++++++++++++++++--
.../static/new/javascript/init_genome_browser.js | 4 ++++
.../css/purescript-genetics-browser.css | 1 +
3 files changed, 28 insertions(+), 2 deletions(-)
create mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index bf90c979..af5d0206 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -376,6 +376,25 @@ class RunMapping(object):
chr_lengths = get_chr_lengths(self.mapping_scale, self.dataset, self.qtl_results_for_browser)
+ #ZS: For zooming into genome browser, need to pass chromosome name instead of number
+ if self.dataset.group.species == "mouse":
+ if self.selected_chr == 20:
+ this_chr = "X"
+ else:
+ this_chr = str(self.selected_chr)
+ elif self.dataset.group.species == "rat":
+ if self.selected_chr == 21:
+ this_chr = "X"
+ else:
+ this_chr = str(self.selected_chr)
+ else:
+ if self.selected_chr == 22:
+ this_chr = "X"
+ elif self.selected_chr == 23:
+ this_chr = "Y"
+ else:
+ this_chr = str(self.selected_chr)
+
if self.mapping_method != "gemma":
if self.score_type == "LRS":
significant_for_browser = self.significant / 4.16
@@ -395,12 +414,14 @@ class RunMapping(object):
num_perm = self.num_perm,
perm_results = self.perm_output,
browser_files = browser_files,
- significant = significant_for_browser
+ significant = significant_for_browser,
+ selected_chr = this_chr
)
else:
self.js_data = dict(
chr_lengths = chr_lengths,
- browser_files = browser_files
+ browser_files = browser_files,
+ selected_chr = this_chr
)
def run_rqtl_plink(self):
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index eba1a69f..2552fb04 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -71,6 +71,10 @@ var config =
coordinateSystem: coordinateSystem,
};
+if (js_data.selected_chr != -1) {
+ config['initialChrs'] = {left: js_data.selected_chr, right: js_data.selected_chr}
+}
+
$('#browser_tab').click(function() {
if ($('#gwas').length == 0){
GenomeBrowser.main(config)();
diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css
new file mode 100644
index 00000000..135292ac
--- /dev/null
+++ b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css
@@ -0,0 +1 @@
+body,html{max-width:100%;overflow-x:hidden}#browser{position:absolute;margin:0}#info-line{border:1px solid #aaa;padding:2px;position:absolute;right:0;top:1px;min-width:14%;font-size:9pt}#controls{visibility:hidden;position:absolute;top:4px;left:100px;z-index:1000}#controls>button{border:1px solid #aaa;border-radius:2px;padding-left:6px;padding-right:6px;height:23px;min-width:20px}button#scrollRight,button#zoomIn{margin-left:-2px;margin-right:4px}#infoBox{position:absolute;display:inline-block;z-index:10000;visibility:hidden;padding:5px;border:2px solid grey;border-radius:5%;background-color:#fff;min-height:100px;min-width:10px;max-width:80%;margin-top:9.7em;font-family:sans-serif}#infoBox>div{float:left;margin:1em 1.2em}#infoBox>div>p{margin:.1em}
\ No newline at end of file
--
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