Skip to content

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
  }
}