Skip to content

Commit f1952fa

Browse files
eweitzeweitz
committed
Merge changes from upstream
2 parents 3c5e538 + 7501f0b commit f1952fa

25 files changed

+786
-51
lines changed

‎README.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44

55
[Ideogram.js](https://eweitz.github.io/ideogram/) is a JavaScript library for [chromosome visualization](https://speakerdeck.com/eweitz/designing-genome-visualizations-with-ideogramjs).
66

7-
Ideogram supports drawing and animating genome-wide datasets for [human](https://eweitz.github.io/ideogram/human), [mouse](https://eweitz.github.io/ideogram/mouse), and [many other eukaryotes](https://eweitz.github.io/ideogram/eukaryotes). The [Ideogram API](https://github.com/eweitz/ideogram/blob/master/api.md) for annotations supports [histograms](https://eweitz.github.io/ideogram/annotations-histogram), [heatmaps](https://eweitz.github.io/ideogram/annotations-heatmap), [overlays](https://eweitz.github.io/ideogram/annotations-overlaid), and points of arbitrary shape and color layered in [tracks](https://eweitz.github.io/ideogram/annotations-tracks). Ideogram can depict haploid, [diploid](https://eweitz.github.io/ideogram/ploidy-basic) or higher ploidy genomes (e.g. plants), as well as aneuploidy, [genetic recombination](https://eweitz.github.io/ideogram/ploidy-recombination), and [homologous features](https://eweitz.github.io/ideogram/homology-basic) between chromosomes.
7+
Ideogram supports drawing and animating genome-wide datasets for [human](https://eweitz.github.io/ideogram/human), [mouse](https://eweitz.github.io/ideogram/mouse), and [many other eukaryotes](https://eweitz.github.io/ideogram/eukaryotes). The [Ideogram API](https://github.com/eweitz/ideogram/blob/master/api.md) for annotations supports [histograms](https://eweitz.github.io/ideogram/annotations-histogram), [heatmaps](https://eweitz.github.io/ideogram/annotations-heatmap), [overlays](https://eweitz.github.io/ideogram/annotations-overlaid), and points of arbitrary shape and color layered in [tracks](https://eweitz.github.io/ideogram/annotations-tracks). The [Ideogram API](https://github.com/eweitz/ideogram/blob/master/api.md) also supports [spanning](https://eweitz.github.io/ideogram/annotations-span) annotations alone, or with [heatmaps and histograms](https://eweitz.github.io/ideogram/annotations-span-heatmap-histogram). Ideogram can depict haploid, [diploid](https://eweitz.github.io/ideogram/ploidy-basic) or higher ploidy genomes (e.g. plants), as well as aneuploidy, [genetic recombination](https://eweitz.github.io/ideogram/ploidy-recombination), and [homologous features](https://eweitz.github.io/ideogram/homology-basic) between chromosomes.
88

99
Ideogram can be embedded as a [reusable component](https://github.com/eweitz/ideogram#usage) in any web page or application, and leverages D3.js and SVG to achieve fast, crisp client-side rendering. You can also integrate Ideogram with JavaScript frameworks like [Angular](https://github.com/eweitz/ideogram/tree/master/examples/angular), [React](https://github.com/eweitz/ideogram/tree/master/examples/react), and [Vue](https://github.com/eweitz/ideogram/tree/master/examples/vue), as well as data science platforms like [R](https://github.com/eweitz/ideogram/tree/master/examples/r) and [Jupyter Notebook](https://github.com/eweitz/ideogram/tree/master/examples/jupyter).
1010

‎api.md

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ String. Optional. OAuth 2.0 access token. Enables authentication and authoriz
8282
Object. Optional. A map associating ancestor labels to colors. Used to color chromosomes from different ancestors in polyploid genomes. Example in [Ploidy, recombination](https://eweitz.github.io/ideogram/ploidy-recombination).
8383

8484
## annotations
85-
Array. Optional. A list of annotation objects. Each annotation object has at least a chromosome name (chr), start coordinate (start), and stop coordinate (stop). Annotation objects can also have a name, color, shape, and track index. Example in [Annotations, basic](https://eweitz.github.io/ideogram/annotations-basic).
85+
Array. Optional. A list of annotation objects. Each annotation object has at least a chromosome name (chr), start coordinate (start), and stop coordinate (stop). Annotation objects can also have a name, color, shape, track index and placement. Positive placement brings the annotations to the bottom/left of the chromosome, whilst negative placement brings it to the top/right. Example in [Annotations, basic](https://eweitz.github.io/ideogram/annotations-basic).
8686

8787
See also [annotationsPath](#annotationspath).
8888

@@ -97,6 +97,10 @@ String. Optional. Default: "tracks".
9797

9898
The layout of this ideogram's annotations. One of "tracks", "heatmap", "histogram", or "overlay".
9999

100+
## annotationsLayout: 'span'
101+
Lay out annotations in spanning tracks beside each chromosome. There can be more than one
102+
track, which is useful for displaying annotations by category (e.g. pathogenic, unknown significance, benign). Example in [Annotations, span](https://eweitz.github.io/ideogram/annotations-span).
103+
100104
### annotationsLayout: 'tracks'
101105
Lay out annotations in tracks beside each chromosome. There can be more than one track, which is useful for displaying annotations by category (e.g. pathogenic, unknown significance, benign). Example in [Annotations, tracks](https://eweitz.github.io/ideogram/annotations-tracks).
102106

@@ -119,7 +123,7 @@ String. Optional. An absolute or relative URL to a JSON file containing annota
119123
See also [annotations](#annotations).
120124

121125
## annotationTracks
122-
Array. Optional. A list of objects with metadata for each track, e.g. DOM `id`, display name, color, shape. Example in [Annotations, tracks](https://eweitz.github.io/ideogram/annotations-tracks).
126+
Array. Optional. A list of objects with metadata for each track, e.g. DOM `id`, display name, color, shape, placement. Example in [Annotations, tracks](https://eweitz.github.io/ideogram/annotations-tracks). If placement is not specified, it is assigned the trackIndex by default. Positive placement brings the annotations to the bottom/left of the chromosome, whilst negative placement brings it to the top/right. The placement of the histogram should have the largest number (either positive or negative) to avoid overlapping of tracks. Example in [Annotations, spanning heatmap and histogram](https://eweitz.github.io/ideogram/annotations-span-heatmap-histogram).
123127

124128
## assembly
125129
String. Optional. Default: latest RefSeq assembly for specified organism. The genome assembly to display. Takes assembly name (e.g. "GRCh37"), RefSeq accession (e.g. "GCF_000306695.2"), or GenBank accession (e.g. "GCA_000005005.5"). Example in [Annotations, histogram](https://eweitz.github.io/ideogram/annotations-histogram).

‎data/annotations/SRR562646.json

Lines changed: 1 addition & 1 deletion
Large diffs are not rendered by default.

‎data/annotations/chr1_span_virtual_cnvs.json

Lines changed: 121 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,121 @@
1+
{
2+
"keys": [
3+
"name",
4+
"start",
5+
"length",
6+
"cn",
7+
"loh"
8+
],
9+
"annots": [
10+
{
11+
"chr": "6",
12+
"annots": [
13+
[
14+
"CN: 1.0251",
15+
1,
16+
2815108,
17+
1.0251,
18+
1
19+
],
20+
[
21+
"CN: 1.9476",
22+
2815110,
23+
9373,
24+
1.9476,
25+
1
26+
],
27+
[
28+
"CN: 1.0555",
29+
2824484,
30+
867,
31+
1.0555,
32+
1
33+
],
34+
[
35+
"CN: 2.0053",
36+
2825352,
37+
39622,
38+
2.0053,
39+
1
40+
],
41+
[
42+
"CN: 1.016",
43+
2864975,
44+
25451276,
45+
1.016,
46+
1
47+
],
48+
[
49+
"CN: 1.9915",
50+
28316252,
51+
1664942,
52+
1.9915,
53+
1
54+
],
55+
[
56+
"CN: 3.3136",
57+
29981195,
58+
0,
59+
3.3136,
60+
1
61+
],
62+
[
63+
"CN: 2.0541",
64+
29981196,
65+
514735,
66+
2.0541,
67+
1
68+
],
69+
[
70+
"CN: 1.0529",
71+
30495932,
72+
4301,
73+
1.0529,
74+
1
75+
],
76+
[
77+
"CN: 2.0509",
78+
30500234,
79+
394989,
80+
2.0509,
81+
1
82+
],
83+
[
84+
"CN: 1.0445",
85+
30895224,
86+
2107400,
87+
1.0445,
88+
1
89+
],
90+
[
91+
"CN: 2.0563",
92+
33002625,
93+
826044,
94+
2.0563,
95+
0
96+
],
97+
[
98+
"CN: 3.0798",
99+
33828670,
100+
479360,
101+
3.0798,
102+
0
103+
],
104+
[
105+
"CN: 2.034",
106+
34308031,
107+
24883879,
108+
2.034,
109+
0
110+
],
111+
[
112+
"CN: 1.9959",
113+
59191911,
114+
111614068,
115+
1.9959,
116+
0
117+
]
118+
]
119+
}
120+
]
121+
}

‎data/annotations/span_heatmap_histogram_virtual.json

Lines changed: 193 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,193 @@
1+
{
2+
"keys": [
3+
"name",
4+
"start",
5+
"length",
6+
"cn",
7+
"loh",
8+
"rna"
9+
],
10+
"annots": [
11+
{
12+
"chr": "1",
13+
"annots": [
14+
[
15+
"CN: 2.1435",
16+
1,
17+
190776,
18+
2.1435,
19+
0,
20+
-3
21+
],
22+
[
23+
"CN: 2.4487",
24+
190778,
25+
18145272,
26+
2.4487,
27+
0,
28+
2
29+
],
30+
[
31+
"CN: 2.0871",
32+
18336051,
33+
85,
34+
2.0871,
35+
0,
36+
1
37+
],
38+
[
39+
"CN: 2.5089",
40+
18336137,
41+
23191072,
42+
2.5089,
43+
0,
44+
-5
45+
],
46+
[
47+
"CN: 2.7998",
48+
41527210,
49+
90,
50+
2.7998,
51+
0,
52+
2.22
53+
],
54+
[
55+
"CN: 2.5607",
56+
41527301,
57+
82078221,
58+
2.5607,
59+
0,
60+
3.9
61+
],
62+
[
63+
"CN: 1.3707",
64+
123605523,
65+
19593339,
66+
1.3707,
67+
1,
68+
1
69+
],
70+
[
71+
"CN: 3.0451",
72+
143198863,
73+
13370044,
74+
3.0451,
75+
1,
76+
-4
77+
],
78+
[
79+
"CN: 3.1856",
80+
156568908,
81+
1,
82+
3.1856,
83+
1,
84+
-5
85+
],
86+
[
87+
"CN: 3.4828",
88+
156568910,
89+
45,
90+
3.4828,
91+
1,
92+
-1
93+
],
94+
[
95+
"CN: 4.2085",
96+
156568956,
97+
26,
98+
4.2085,
99+
1,
100+
5
101+
],
102+
[
103+
"CN: 4.3929",
104+
156568983,
105+
32,
106+
4.3929,
107+
1,
108+
2
109+
],
110+
[
111+
"CN: 3.2331",
112+
156569016,
113+
755261,
114+
3.2331,
115+
1,
116+
3
117+
],
118+
[
119+
"CN: 3.4452",
120+
157324278,
121+
36243,
122+
3.4452,
123+
1,
124+
3
125+
],
126+
[
127+
"CN: 3.2047",
128+
157360522,
129+
592359,
130+
3.2047,
131+
1,
132+
1
133+
],
134+
[
135+
"CN: 3.4436",
136+
157952882,
137+
15,
138+
3.4436,
139+
1,
140+
5
141+
],
142+
[
143+
"CN: 3.1231",
144+
157952898,
145+
10744011,
146+
3.1231,
147+
1,
148+
1
149+
],
150+
[
151+
"CN: 1.5717",
152+
168696910,
153+
13690908,
154+
1.5717,
155+
1,
156+
1.04
157+
],
158+
[
159+
"CN: 1.0007",
160+
182387819,
161+
4768035,
162+
1.0007,
163+
1,
164+
2
165+
],
166+
[
167+
"CN: 1.2406",
168+
187155855,
169+
633,
170+
1.2406,
171+
1,
172+
3.22
173+
],
174+
[
175+
"CN: 0.9875",
176+
187156489,
177+
7616168,
178+
0.9875,
179+
1,
180+
3.96
181+
],
182+
[
183+
"CN: 1.4343",
184+
194772658,
185+
54183764,
186+
1.4343,
187+
1,
188+
4
189+
]
190+
]
191+
}
192+
]
193+
}

‎dist/js/ideogram.min.js.map

Lines changed: 1 addition & 1 deletion
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

‎examples/vanilla/annotations-basic.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ <h1>Annotations, basic | Ideogram</h1>
3131
name: 'BRCA1',
3232
chr: '17',
3333
start: 43044294,
34-
stop: 43125482
34+
stop: 43125482,
3535
}]
3636
};
3737

‎examples/vanilla/annotations-histogram.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -201,4 +201,4 @@ <h1>Annotations, histogram | Ideogram</h1>
201201
var ideogram = new Ideogram(config);
202202
</script>
203203
</body>
204-
</html>
204+
</html>

0 commit comments

Comments
 (0)