Small non-zero values for size scale are not visible

In Vega-Lite 2.x, if you encode a quantity with size and that quantity has elements with value zero, those points do not appear on the plot with the default scale:

{
  "$schema": "https://vega.github.io/schema/vega-lite/v2.json",
  "data": {
    "url": "https://vega.github.io/vega-datasets/data/seattle-weather.csv"
  },
  "encoding": {
    "color": {
      "field": "weather",
      "type": "nominal"
    },
    "size": {
      "field": "precipitation",
      "type": "quantitative"
    },
    "x": {
      "field": "temp_min",
      "type": "quantitative"
    },
    "y": {
      "field": "temp_max",
      "type": "quantitative"
    }
  },
  "mark": "point"
}

In Vega-Lite 1.x, this was not the case; here’s the result of the above spec with VL1:

In VL2, you can fix this by setting the size scale domain to start at a negative number:

{
  "$schema": "https://vega.github.io/schema/vega-lite/v2.json",
  "data": {
    "url": "https://vega.github.io/vega-datasets/data/seattle-weather.csv"
  },
  "encoding": {
    "color": {
      "field": "weather",
      "type": "nominal"
    },
    "size": {
      "field": "precipitation",
      "type": "quantitative",
      "scale": {"domain": [-1, 50]}
    },
    "x": {
      "field": "temp_min",
      "type": "quantitative"
    },
    "y": {
      "field": "temp_max",
      "type": "quantitative"
    }
  },
  "mark": "point"
}

I think that silently hiding valid data should be considered a bug, and that the domain should default to something like what is in the final panel.

[domoritz]

Something like

{
  "$schema": "https://vega.github.io/schema/vega/v3.0.json",
  "autosize": "pad",
  "padding": 5,
  "width": 500,
  "height": 500,
  "style": "cell",
  "data": [
    {
      "name": "source_0",
      "url": "https://vega.github.io/vega-datasets/data/seattle-weather.csv",
      "format": {
        "type": "csv",
        "parse": {
          "precipitation": "number",
          "temp_min": "number",
          "temp_max": "number"
        },
        "delimiter": ","
      },
      "transform": [
        {
          "type": "filter",
          "expr": "datum[\"precipitation\"] !== null && !isNaN(datum[\"precipitation\"]) && datum[\"temp_min\"] !== null && !isNaN(datum[\"temp_min\"]) && datum[\"temp_max\"] !== null && !isNaN(datum[\"temp_max\"])"
        }
      ]
    }
  ],
  "marks": [
    {
      "name": "marks",
      "type": "symbol",
      "style": ["point"],
      "from": {"data": "source_0"},
      "encode": {
        "update": {
          "opacity": {"value": 0.7},
          "fill": {
            "signal": "scale('size', datum.precipitation) < 1 ? scale('color', datum.weather) : 'transparent'"
          },
          "stroke": {"scale": "color", "field": "weather"},
          "x": {"scale": "x", "field": "temp_min"},
          "y": {"scale": "y", "field": "temp_max"},
          "size": {
            "signal": "scale('size', datum.precipitation) < 1 ? 1 : scale('size', datum.precipitation)"
          }
        }
      }
    }
  ],
  "scales": [
    {
      "name": "x",
      "type": "linear",
      "domain": {"data": "source_0", "field": "temp_min"},
      "range": [0, {"signal": "width"}],
      "nice": true,
      "zero": true
    },
    {
      "name": "y",
      "type": "linear",
      "domain": {"data": "source_0", "field": "temp_max"},
      "range": [{"signal": "height"}, 0],
      "nice": true,
      "zero": true
    },
    {
      "name": "color",
      "type": "ordinal",
      "domain": {"data": "source_0", "field": "weather", "sort": true},
      "range": "category"
    },
    {
      "name": "size",
      "type": "linear",
      "domain": {"data": "source_0", "field": "precipitation"},
      "range": [0.1, 361],
      "nice": false,
      "zero": true
    }
  ],
  "axes": [
    {
      "scale": "x",
      "orient": "bottom",
      "title": "temp_min",
      "labelFlush": true,
      "labelOverlap": true,
      "tickCount": {"signal": "ceil(width/40)"},
      "zindex": 1
    },
    {
      "scale": "x",
      "orient": "bottom",
      "grid": true,
      "tickCount": {"signal": "ceil(width/40)"},
      "gridScale": "y",
      "domain": false,
      "labels": false,
      "maxExtent": 0,
      "minExtent": 0,
      "ticks": false,
      "zindex": 0
    },
    {
      "scale": "y",
      "orient": "left",
      "title": "temp_max",
      "labelOverlap": true,
      "tickCount": {"signal": "ceil(height/40)"},
      "zindex": 1
    },
    {
      "scale": "y",
      "orient": "left",
      "grid": true,
      "tickCount": {"signal": "ceil(height/40)"},
      "gridScale": "x",
      "domain": false,
      "labels": false,
      "maxExtent": 0,
      "minExtent": 0,
      "ticks": false,
      "zindex": 0
    }
  ],
  "legends": [
    {
      "stroke": "color",
      "title": "weather",
      "encode": {"symbols": {"update": {"opacity": {"value": 0.7}}}}
    },
    {
      "size": "size",
      "title": "precipitation",
      "encode": {"symbols": {"update": {"opacity": {"value": 0.7}}}}
    }
  ],
  "config": {"axisY": {"minExtent": 30}}
}

[kanitw]

I wonder whether there is a way to get filled circles of radius 1 for the smallest circles instead of hollow circles.

Yes, you can add production rule, instead of making scale inaccurate.