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Stack

The "stack" transform computes a stacked layout. Stacked bar plots and sequence logos are some of its applications.

Parameters

as Required

Type: array

Fields to write the stacked values.

Default: ["y0", "y1"]

baseField

Type: string (field name)

The field that contains the base or amino acid. Used for information content calculation when the offset is "information". The data objects that have null in the baseField are considered gaps and they are taken into account when scaling the the locus' information content.

cardinality

Type: number

Cardinality, e.g., the number if distinct bases or amino acids. Used for information content calculation when the offset is "information".

Default: 4

field

Type: string (field name)

The field to stack. If no field is defined, a constant value of one is assumed.

groupby Required

Type: array

The fields to be used for forming groups for different stacks.

offset

Type: string

How to offset the values in a stack. "zero" (default) starts stacking at 0. "center" centers the values around zero. "normalize" computes intra-stack percentages and normalizes the values to the range of [0, 1]. "information" computes a layout for a sequence logo. The total height of the stack reflects the group's information content.

sort

Type: CompareParams

The sort order of data in each stack.

Examples

Stacked bar plot

{
  "data": {
    "values": [
      { "x": 1, "q": "A", "z": 7 },
      { "x": 1, "q": "B", "z": 3 },
      { "x": 1, "q": "C", "z": 10 },
      { "x": 2, "q": "A", "z": 8 },
      { "x": 2, "q": "B", "z": 5 },
      { "x": 3, "q": "B", "z": 10 }
    ]
  },
  "transform": [
    {
      "type": "stack",
      "field": "z",
      "groupby": ["x"]
    }
  ],
  "mark": "rect",
  "encoding": {
    "x": { "field": "x", "type": "nominal", "band": 0.8 },
    "y": { "field": "y0", "type": "quantitative" },
    "y2": { "field": "y1" },
    "color": { "field": "q", "type": "nominal" }
  }
}

{
  "data": {
    "values": [
      { "pos": 1, "base": "A", "count": 2 },
      { "pos": 1, "base": "C", "count": 3 },
      { "pos": 1, "base": "T", "count": 5 },
      { "pos": 2, "base": "A", "count": 7 },
      { "pos": 2, "base": "C", "count": 3 },
      { "pos": 3, "base": "A", "count": 10 },
      { "pos": 4, "base": "T", "count": 9 },
      { "pos": 4, "base": "G", "count": 1 },
      { "pos": 5, "base": "G", "count": 8 },
      { "pos": 6, "base": "G", "count": 7 }
    ]
  },
  "transform": [
    {
      "type": "stack",
      "field": "count",
      "groupby": ["pos"],
      "offset": "information",
      "as": ["_y0", "_y1"],
      "baseField": "base",
      "sort": { "field": "count", "order": "ascending" }
    }
  ],
  "encoding": {
    "x": { "field": "pos", "type": "index" },
    "y": {
      "field": "_y0",
      "type": "quantitative",
      "scale": { "domain": [0, 2] },
      "title": "Information"
    },
    "y2": { "field": "_y1" },
    "text": { "field": "base", "type": "nominal" },
    "color": {
      "field": "base",
      "type": "nominal",
      "scale": {
        "type": "ordinal",
        "domain": ["A", "C", "T", "G"],
        "range": ["#7BD56C", "#FF9B9B", "#86BBF1", "#FFC56C"]
      }
    }
  },
  "mark": {
    "type": "text",
    "font": "Source Sans Pro",
    "fontWeight": 700,
    "size": 100,
    "squeeze": true,
    "fitToBand": true,

    "paddingX": 0,
    "paddingY": 0,

    "logoLetters": true
  }
}