etowahadams
commented
10 months ago Thanks for submitting and issue! This does seem to be a bug.
In the short term, you might get a similar desired effect by changing "point" to "bar".
Here is the spec to reproduce. Change "point" to "line" or "bar" to observe the differences. We expect "line" to behave like "point" and"bar" (not visible when zoomed out) but unexpectedly it is visible at all levels of zoom.
{
"xDomain": {"chromosome": "chr13", "interval": [31500000, 33150000]},
"centerRadius": 0.1,
"layout": "linear",
"spacing": 0,
"alignment": "stack",
"tracks": [
{
"alignment": "overlay",
"data": {
"url": "https://server.gosling-lang.org/api/v1/tileset_info/?d=clinvar-beddb",
"type": "beddb",
"genomicFields": [
{"index": 1, "name": "start"},
{"index": 2, "name": "end"}
],
"valueFields": [
{"index": 7, "name": "significance", "type": "nominal"}
]
},
"tracks": [
{
"mark": "bar",
"x": {"field": "start", "type": "genomic"},
"y": {
"field": "significance",
"type": "nominal",
"domain": [
"Pathogenic",
"Pathogenic/Likely_pathogenic",
"Likely_pathogenic",
"Uncertain_significance",
"Likely_benign",
"Benign/Likely_benign",
"Benign"
],
"baseline": "Uncertain_significance",
"range": [150, 20]
},
"size": {"value": 1},
"color": {"value": "lightgray"},
"stroke": {"value": "lightgray"},
"strokeWidth": {"value": 1},
"opacity": {"value": 0.3},
"visibility": [
{
"measure": "zoomLevel",
"target": "mark",
"threshold": 100000,
"operation": "LT",
"transitionPadding": 100000
}
]
},
{
"mark": "point",
"x": {"field": "start", "type": "genomic"},
"row": {
"field": "significance",
"type": "nominal",
"domain": [
"Pathogenic",
"Pathogenic/Likely_pathogenic",
"Likely_pathogenic",
"Uncertain_significance",
"Likely_benign",
"Benign/Likely_benign",
"Benign"
]
},
"size": {"value": 7},
"opacity": {"value": 0.8},
"visibility": [
{
"measure": "zoomLevel",
"target": "mark",
"threshold": 1000000,
"operation": "LT",
"transitionPadding": 1000000
}
]
},
{
"data": {
"url": "https://server.gosling-lang.org/api/v1/tileset_info/?d=clinvar-multivec",
"type": "multivec",
"row": "significance",
"column": "position",
"value": "count",
"categories": [
"Benign",
"Benign/Likely_benign",
"Likely_benign",
"Uncertain_significance",
"Likely_pathogenic",
"Pathogenic/Likely_pathogenic",
"Pathogenic"
],
"binSize": 4
},
"mark": "bar",
"x": {"field": "start", "type": "genomic"},
"xe": {"field": "end", "type": "genomic"},
"y": {"field": "count", "type": "quantitative", "axis": "none"},
"color": {
"field": "significance",
"type": "nominal",
"domain": [
"Pathogenic",
"Pathogenic/Likely_pathogenic",
"Likely_pathogenic",
"Uncertain_significance",
"Likely_benign",
"Benign/Likely_benign",
"Benign"
],
"range": [
"#CB3B8C",
"#CB71A3",
"#CB96B3",
"gray",
"#029F73",
"#5A9F8C",
"#5A9F8C"
],
"legend": true
},
"visibility": [
{
"measure": "zoomLevel",
"target": "mark",
"threshold": 500000,
"operation": "GT",
"transitionPadding": 500000
}
]
}
],
"color": {
"field": "significance",
"type": "nominal",
"domain": [
"Pathogenic",
"Pathogenic/Likely_pathogenic",
"Likely_pathogenic",
"Uncertain_significance",
"Likely_benign",
"Benign/Likely_benign",
"Benign"
],
"range": [
"#CB3B8C",
"#CB71A3",
"#CB96B3",
"gray",
"#029F73",
"#5A9F8C",
"#5A9F8C"
]
},
"width": 800,
"height": 150
}
]
}
zoommark.webm
I am not sure if this intended or not. But it seems that the line mark is not working with semantic visibility.
The relevant section in the spec is this:
"visibility": [ { "measure": "zoomLevel", "target": "mark", "threshold": 1000000, "operation": "LT", "transitionPadding": 1000000 } ]