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Merge pull request #68 from gwaygenomics/add-dvc
Adding plate profiles to DVC
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| /config.local | ||
| /tmp | ||
| /cache |
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| @@ -0,0 +1,4 @@ | ||
| [core] | ||
| remote = cellpainting-datasets | ||
| ['remote "cellpainting-datasets"'] | ||
| url = s3://cellpainting-datasets/lincs-cell-painting/.dvc/cache |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| { | ||
| "$schema": "https://vega.github.io/schema/vega-lite/v4.json", | ||
| "data": { | ||
| "values": "<DVC_METRIC_DATA>" | ||
| }, | ||
| "title": "<DVC_METRIC_TITLE>", | ||
| "facet": { | ||
| "field": "rev", | ||
| "type": "nominal" | ||
| }, | ||
| "spec": { | ||
| "transform": [ | ||
| { | ||
| "aggregate": [ | ||
| { | ||
| "op": "count", | ||
| "as": "xy_count" | ||
| } | ||
| ], | ||
| "groupby": [ | ||
| "<DVC_METRIC_Y>", | ||
| "<DVC_METRIC_X>" | ||
| ] | ||
| }, | ||
| { | ||
| "impute": "xy_count", | ||
| "groupby": [ | ||
| "rev", | ||
| "<DVC_METRIC_Y>" | ||
| ], | ||
| "key": "<DVC_METRIC_X>", | ||
| "value": 0 | ||
| }, | ||
| { | ||
| "impute": "xy_count", | ||
| "groupby": [ | ||
| "rev", | ||
| "<DVC_METRIC_X>" | ||
| ], | ||
| "key": "<DVC_METRIC_Y>", | ||
| "value": 0 | ||
| }, | ||
| { | ||
| "joinaggregate": [ | ||
| { | ||
| "op": "max", | ||
| "field": "xy_count", | ||
| "as": "max_count" | ||
| } | ||
| ], | ||
| "groupby": [] | ||
| }, | ||
| { | ||
| "calculate": "datum.xy_count / datum.max_count", | ||
| "as": "percent_of_max" | ||
| } | ||
| ], | ||
| "encoding": { | ||
| "x": { | ||
| "field": "<DVC_METRIC_X>", | ||
| "type": "nominal", | ||
| "sort": "ascending", | ||
| "title": "<DVC_METRIC_X_LABEL>" | ||
| }, | ||
| "y": { | ||
| "field": "<DVC_METRIC_Y>", | ||
| "type": "nominal", | ||
| "sort": "ascending", | ||
| "title": "<DVC_METRIC_Y_LABEL>" | ||
| } | ||
| }, | ||
| "layer": [ | ||
| { | ||
| "mark": "rect", | ||
| "width": 300, | ||
| "height": 300, | ||
| "encoding": { | ||
| "color": { | ||
| "field": "xy_count", | ||
| "type": "quantitative", | ||
| "title": "", | ||
| "scale": { | ||
| "domainMin": 0, | ||
| "nice": true | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "mark": "text", | ||
| "encoding": { | ||
| "text": { | ||
| "field": "xy_count", | ||
| "type": "quantitative" | ||
| }, | ||
| "color": { | ||
| "condition": { | ||
| "test": "datum.percent_of_max > 0.5", | ||
| "value": "white" | ||
| }, | ||
| "value": "black" | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| { | ||
| "$schema": "https://vega.github.io/schema/vega-lite/v4.json", | ||
| "data": { | ||
| "values": "<DVC_METRIC_DATA>" | ||
| }, | ||
| "title": "<DVC_METRIC_TITLE>", | ||
| "facet": { | ||
| "field": "rev", | ||
| "type": "nominal" | ||
| }, | ||
| "spec": { | ||
| "transform": [ | ||
| { | ||
| "aggregate": [ | ||
| { | ||
| "op": "count", | ||
| "as": "xy_count" | ||
| } | ||
| ], | ||
| "groupby": [ | ||
| "<DVC_METRIC_Y>", | ||
| "<DVC_METRIC_X>" | ||
| ] | ||
| }, | ||
| { | ||
| "impute": "xy_count", | ||
| "groupby": [ | ||
| "rev", | ||
| "<DVC_METRIC_Y>" | ||
| ], | ||
| "key": "<DVC_METRIC_X>", | ||
| "value": 0 | ||
| }, | ||
| { | ||
| "impute": "xy_count", | ||
| "groupby": [ | ||
| "rev", | ||
| "<DVC_METRIC_X>" | ||
| ], | ||
| "key": "<DVC_METRIC_Y>", | ||
| "value": 0 | ||
| }, | ||
| { | ||
| "joinaggregate": [ | ||
| { | ||
| "op": "sum", | ||
| "field": "xy_count", | ||
| "as": "sum_y" | ||
| } | ||
| ], | ||
| "groupby": [ | ||
| "<DVC_METRIC_Y>" | ||
| ] | ||
| }, | ||
| { | ||
| "calculate": "datum.xy_count / datum.sum_y", | ||
| "as": "percent_of_y" | ||
| } | ||
| ], | ||
| "encoding": { | ||
| "x": { | ||
| "field": "<DVC_METRIC_X>", | ||
| "type": "nominal", | ||
| "sort": "ascending", | ||
| "title": "<DVC_METRIC_X_LABEL>" | ||
| }, | ||
| "y": { | ||
| "field": "<DVC_METRIC_Y>", | ||
| "type": "nominal", | ||
| "sort": "ascending", | ||
| "title": "<DVC_METRIC_Y_LABEL>" | ||
| } | ||
| }, | ||
| "layer": [ | ||
| { | ||
| "mark": "rect", | ||
| "width": 300, | ||
| "height": 300, | ||
| "encoding": { | ||
| "color": { | ||
| "field": "percent_of_y", | ||
| "type": "quantitative", | ||
| "title": "", | ||
| "scale": { | ||
| "domain": [ | ||
| 0, | ||
| 1 | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "mark": "text", | ||
| "encoding": { | ||
| "text": { | ||
| "field": "percent_of_y", | ||
| "type": "quantitative", | ||
| "format": ".2f" | ||
| }, | ||
| "color": { | ||
| "condition": { | ||
| "test": "datum.percent_of_y > 0.5", | ||
| "value": "white" | ||
| }, | ||
| "value": "black" | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| { | ||
| "$schema": "https://vega.github.io/schema/vega-lite/v4.json", | ||
| "data": { | ||
| "values": "<DVC_METRIC_DATA>" | ||
| }, | ||
| "title": "<DVC_METRIC_TITLE>", | ||
| "width": 300, | ||
| "height": 300, | ||
| "mark": { | ||
| "type": "line" | ||
| }, | ||
| "encoding": { | ||
| "x": { | ||
| "field": "<DVC_METRIC_X>", | ||
| "type": "quantitative", | ||
| "title": "<DVC_METRIC_X_LABEL>" | ||
| }, | ||
| "y": { | ||
| "field": "<DVC_METRIC_Y>", | ||
| "type": "quantitative", | ||
| "title": "<DVC_METRIC_Y_LABEL>", | ||
| "scale": { | ||
| "zero": false | ||
| } | ||
| }, | ||
| "color": { | ||
| "field": "rev", | ||
| "type": "nominal" | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| { | ||
| "$schema": "https://vega.github.io/schema/vega-lite/v4.json", | ||
| "data": { | ||
| "values": "<DVC_METRIC_DATA>" | ||
| }, | ||
| "title": "<DVC_METRIC_TITLE>", | ||
| "width": 300, | ||
| "height": 300, | ||
| "layer": [ | ||
| { | ||
| "encoding": { | ||
| "x": { | ||
| "field": "<DVC_METRIC_X>", | ||
| "type": "quantitative", | ||
| "title": "<DVC_METRIC_X_LABEL>" | ||
| }, | ||
| "y": { | ||
| "field": "<DVC_METRIC_Y>", | ||
| "type": "quantitative", | ||
| "title": "<DVC_METRIC_Y_LABEL>", | ||
| "scale": { | ||
| "zero": false | ||
| } | ||
| }, | ||
| "color": { | ||
| "field": "rev", | ||
| "type": "nominal" | ||
| } | ||
| }, | ||
| "layer": [ | ||
| { | ||
| "mark": "line" | ||
| }, | ||
| { | ||
| "selection": { | ||
| "label": { | ||
| "type": "single", | ||
| "nearest": true, | ||
| "on": "mouseover", | ||
| "encodings": [ | ||
| "x" | ||
| ], | ||
| "empty": "none", | ||
| "clear": "mouseout" | ||
| } | ||
| }, | ||
| "mark": "point", | ||
| "encoding": { | ||
| "opacity": { | ||
| "condition": { | ||
| "selection": "label", | ||
| "value": 1 | ||
| }, | ||
| "value": 0 | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "transform": [ | ||
| { | ||
| "filter": { | ||
| "selection": "label" | ||
| } | ||
| } | ||
| ], | ||
| "layer": [ | ||
| { | ||
| "mark": { | ||
| "type": "rule", | ||
| "color": "gray" | ||
| }, | ||
| "encoding": { | ||
| "x": { | ||
| "field": "<DVC_METRIC_X>", | ||
| "type": "quantitative" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "encoding": { | ||
| "text": { | ||
| "type": "quantitative", | ||
| "field": "<DVC_METRIC_Y>" | ||
| }, | ||
| "x": { | ||
| "field": "<DVC_METRIC_X>", | ||
| "type": "quantitative" | ||
| }, | ||
| "y": { | ||
| "field": "<DVC_METRIC_Y>", | ||
| "type": "quantitative" | ||
| } | ||
| }, | ||
| "layer": [ | ||
| { | ||
| "mark": { | ||
| "type": "text", | ||
| "align": "left", | ||
| "dx": 5, | ||
| "dy": -5 | ||
| }, | ||
| "encoding": { | ||
| "color": { | ||
| "type": "nominal", | ||
| "field": "rev" | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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