Data Input

GenomeSpy inputs tabular data as CSV, TSV, or JSON files. Currently, common bioinformatic data formats such as BED or BigWig are not directly supported. They must be first converted into one of the tabular formats above.

GenomeSpy can load data from external files or use inline data. You can also use generators to generate data on the fly and modify them using transforms.

The data property of the view specification describes a data source. The following example loads a tab-delimited file. By default, the format is inferred from the file extension. However, in bioinformatics, .csv files are often tab-delimited and the TSV format must be specified explicitly.

  "data": {
    "url": "fileWithTabs.csv",
    "format": { "type": "tsv" }

With the exception of the geographical formats, the data property of GenomeSpy is identical to Vega-Lite's data property.

Type inference

GenomeSpy uses vega-loader to parse tabular data and infer its data types. Vega-loader is sometimes overly eager to interpret the text as a date. In such cases, the field types need to be specified explicitly. On the other hand, explicit type specification also has a significant positive effect on parsing performance.

TODO: Grouped data, ungroup transform