Display up to N data points for numeric layers: N =
+
+
+
+
+
+
+
+
+ Scale
+
+
+
+
Dynamic scale interval
+
+
+
+
+
+
+
Genome scale interval:
+
+
+
+
+
+
+
+
+ Gene arrows
+
Change colors of genes based on their functional annotations. You can also
+ manually color genes temporarily. First, right-click on a gene. It will add the gene into the list below with
+ a default color. Then, you can use the color picker next to it to set a color manually.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Only show categories in the current render window:
+
+
+
+
+
+
Filter:
+
+
+
+
+
+
Sort:
+
+
+
+
+
+
+
+
+
+
+
+
Rule:
+
+ All
+ Name contains
+ Count
+
+
+
+
+
+
+
Color:
+
+
+
+
+
+
+
Assign random color
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Color
+
+
Annotation
+
+
+
+
+
+
+ Gene links
+
+
+
+
+
+
+
+
TODO: Color table for shades (with opacity option too?)
+
+ Labels
+
+
+
+
Show genome labels
+
+
+
+
+
+
+
Genome label size:
+
+
+
+
Genome label color:
+
+
+
+
+
+
Show gene labels:
+
+
+
+
+
+
+
Link gene label/color source:
+
+
+
+
+
+
Gene label source:
+
+
+
+
+
+
+
+
Gene label size:
+
+
+
+
Gene label color:
+
+
+
+
+
+
Gene label position:
+
+
+
+
+
+
+
+
Gene label angle:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ◀QUERY
+
+
+ Search!
+
+
+
+
Category:
+
+
+
+
+
+
Function Name:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Gene ID
+
Genome
+
Start
+
Stop
+
Action
+
+
+
+
+ Bookmarks
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ◀MOUSE
+
+
+
Gene Call
+
+
+
ID
+
Source
+
Length
+
Direction
+
Start
+
Stop
+
Call type
+
+
+
+
+
Annotations
+
+
+
Source
+
Accession
+
Annotation
+
+
+
+
+
+
+
+
+
+
+
+
Load State
+
+
+
+
+
+
Last modified: n/a
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Save State
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/anvio/data/interactive/js/animations.js b/anvio/data/interactive/js/animations.js
index 16b99afbf3..e771bc2a12 100644
--- a/anvio/data/interactive/js/animations.js
+++ b/anvio/data/interactive/js/animations.js
@@ -1,3 +1,21 @@
+/**
+ * Functions for panel animations.
+ *
+ * Authors: Özcan Esen
+ *
+ * Copyright 2015-2021, The anvi'o project (http://anvio.org)
+ *
+ * Anvi'o is a free software. You can redistribute this program
+ * and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with anvi'o. If not, see .
+ *
+ * @license GPL-3.0+
+ */
+
var ANIMATIONS_ENABLED = true;
var SLIDE_INTERVAL = 4;
var SLIDE_STEP_SIZE = 15;
@@ -11,7 +29,7 @@ function toggleLeftPanel() {
is_left_panel_sliding = true;
if ($('#panel-left').is(':visible')) {
- var animation_frame = function(){
+ var animation_frame = function(){
if (ANIMATIONS_ENABLED && $('#panel-left')[0].getBoundingClientRect().right > 0) {
$('#panel-left').css('left', parseInt($('#panel-left').css('left')) - SLIDE_STEP_SIZE);
$('#toggle-panel-left').css('left', $('#sidebar')[0].getBoundingClientRect().right + 'px');
@@ -28,7 +46,7 @@ function toggleLeftPanel() {
animation_frame();
} else {
$('#panel-left').show();
- var animation_frame = function(){
+ var animation_frame = function(){
if (ANIMATIONS_ENABLED && $('#panel-left')[0].getBoundingClientRect().left < 0) {
$('#panel-left').css('left', parseInt($('#panel-left').css('left')) + SLIDE_STEP_SIZE);
$('#toggle-panel-left').css('left', $('#sidebar')[0].getBoundingClientRect().right + 'px');
@@ -50,7 +68,7 @@ function toggleRightPanel(name) {
['#mouse_hover_panel', '#description-panel', '#news-panel'].forEach(function(right_panel) {
if (right_panel == name)
return;
-
+
$(right_panel).hide();
});
diff --git a/anvio/data/interactive/js/area-zoom.js b/anvio/data/interactive/js/area-zoom.js
index 24b97881a1..40d1805e97 100644
--- a/anvio/data/interactive/js/area-zoom.js
+++ b/anvio/data/interactive/js/area-zoom.js
@@ -1,3 +1,22 @@
+/**
+ * Zooming in an out.
+ *
+ * Authors: Özcan Esen
+ *
+ * Copyright 2015-2021, The anvi'o project (http://anvio.org)
+ *
+ * Anvi'o is a free software. You can redistribute this program
+ * and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with anvi'o. If not, see .
+ *
+ * @license GPL-3.0+
+ */
+
+
var mouse_event_origin_x = 0;
var mouse_event_origin_y = 0;
@@ -9,8 +28,8 @@ function initialize_area_zoom() {
var viewport = document.getElementById('svg');
viewport.addEventListener('mousedown',
- function(event) {
- dragging = false;
+ function(event) {
+ dragging = false;
document.activeElement.blur();
mouse_event_origin_x = event.clientX;
@@ -28,11 +47,11 @@ function initialize_area_zoom() {
}
});
- viewport.addEventListener('mousemove',
+ viewport.addEventListener('mousemove',
function(event) {
if (Math.abs(mouse_event_origin_x - event.clientX) + Math.abs(mouse_event_origin_y - event.clientY) > 2)
{
- dragging = true;
+ dragging = true;
}
if (event.shiftKey && drawing_zoom)
@@ -56,25 +75,25 @@ function initialize_area_zoom() {
}
});
- viewport.addEventListener('mouseup',
+ viewport.addEventListener('mouseup',
function() {
if (drawing_zoom)
{
var zoom_rect = document.getElementById('divzoom').getBoundingClientRect();
-
+
if (zoom_rect.width > 2 && zoom_rect.height > 2)
{
var _dx = (parseInt("0" + $('#svg').position().left) + (VIEWER_WIDTH / 2)) - (zoom_rect.left + zoom_rect.width / 2);
var _dy = (parseInt("0" + $('#svg').position().top) + (VIEWER_HEIGHT / 2)) - (zoom_rect.top + zoom_rect.height / 2);
- pan(_dx,_dy);
+ pan(_dx,_dy);
zoom(Math.min(VIEWER_WIDTH / zoom_rect.width, VIEWER_HEIGHT / zoom_rect.height));
}
}
clearTextSelection();
- drawing_zoom=false;
- zoomBox = {};
- $('#divzoom').hide();
+ drawing_zoom=false;
+ zoomBox = {};
+ $('#divzoom').hide();
});
}
diff --git a/anvio/data/interactive/js/bin.js b/anvio/data/interactive/js/bin.js
index 207401be0d..63793ac59e 100644
--- a/anvio/data/interactive/js/bin.js
+++ b/anvio/data/interactive/js/bin.js
@@ -1,11 +1,11 @@
/**
* Draw bins, bin labels stuff.
*
- * Author: Özcan Esen
- * Credits: A. Murat Eren
- * Copyright 2017, The anvio Project
+ * Authors: Özcan Esen
+ * A. Murat Eren
*
- * This file is part of anvi'o ().
+ *
+ * Copyright 2015-2021, The anvi'o project (http://anvio.org)
*
* Anvi'o is a free software. You can redistribute this program
* and/or modify it under the terms of the GNU General Public
diff --git a/anvio/data/interactive/js/charts.js b/anvio/data/interactive/js/charts.js
index b1947117be..fd37cbf0ee 100644
--- a/anvio/data/interactive/js/charts.js
+++ b/anvio/data/interactive/js/charts.js
@@ -1,11 +1,14 @@
/**
* Javascript library to visualize anvi'o charts
*
- * Author: A. Murat Eren
- * Credits: Özcan Esen, Gökmen Göksel, Tobias Paczian.
- * Copyright 2015, The anvio Project
+ * Authors: A. Murat Eren
+ * Ozcan Esen
+ * Isaac Fink
+ * Matthew Klein
+ * Gökmen Göksel
+ * Tobias Paczian
*
- * This file is part of anvi'o ().
+ * Copyright 2015-2021, The anvi'o project (http://anvio.org)
*
* Anvi'o is a free software. You can redistribute this program
* and/or modify it under the terms of the GNU General Public
@@ -51,10 +54,8 @@ var gene_offset_y = 0;
var select_boxes = {};
var curr_height;
var show_cags_in_split = true;
-
-var mcags;
-
-var cog_annotated = false, kegg_annotated = false;
+var thresh_count_gene_colors = 1;
+var order_gene_colors_by_count = true;
function loadAll() {
info("Initiated");
@@ -218,21 +219,6 @@ function loadAll() {
info("Checking for gene functional annotations");
geneParser = new GeneParser(genes);
- geneParser["data"].forEach(function(gene) {
- if(gene.functions != null) {
- if(gene.functions.hasOwnProperty("COG20_CATEGORY")) {
- gene.functions["COG_CATEGORY"] = gene.functions["COG20_CATEGORY"];
- gene.functions["COG_FUNCTION"] = gene.functions["COG20_FUNCTION"];
- } else if(gene.functions.hasOwnProperty("COG14_CATEGORY")) {
- gene.functions["COG_CATEGORY"] = gene.functions["COG14_CATEGORY"];
- gene.functions["COG_FUNCTION"] = gene.functions["COG14_FUNCTION"];
- }
-
- if(gene.functions.hasOwnProperty("COG_CATEGORY")) cog_annotated = true;
- if(gene.functions.hasOwnProperty("KEGG_Class")) kegg_annotated = true;
- if(cog_annotated && kegg_annotated) return;
- }
- });
if(!state['highlight-genes']) state['highlight-genes'] = {};
state['large-indel'] = 10;
@@ -279,25 +265,14 @@ function loadAll() {
state['source-colors'] = default_source_colors;
}
generateFunctionColorTable(state['source-colors'], "Source", highlight_genes=state['highlight-genes'], show_cags_in_split);
- mcags = Object.keys(default_source_colors);
- if(cog_annotated) {
- $('#gene_color_order').append($('