Configuration Load Morpheus with a pre-configured matrix

There are two options to loading a pre-configured matrix.

1. Pass the request parameters json, a URI encoded JSON configuration object, or url, a URL to a JSON configuration file, to https://software.broadinstitute.org/morpheus/ (can be embedded using an iframe).
Note that the correct HTTP CORS headers must be set if any of your resources are hosted on a different domain.

2. Include morpheus-latest.min.css, morpheus-external-latest.min.js, morpheus-latest.min.js in your HTML. Construct a new morpheus.HeatMap object with the el parameter, the element in which to render the heat map.

• dataset
  A File or URL to one of the accepted file formats.
  Can also be an array of files or URLs in which case the datasets are combined by matching on column ids.
  Also be can specified in JSON format

  • rows Number
    Number of rows in the dataset
  • columns Number
    Number of columns in the dataset
  • seriesArrays[[number, object]]
    Each series contains an array of arrays in row-major order.
  • seriesNames [string]
    Array of series names
  • seriesDataTypes [string]
    Array of series data types
  • rowMetadataModel Object with the key "vectors"
    Contains dataset row metadata
    • vectors Array
      Array of objects with the keys "name" and "array".
  • columnMetadataModel Object with the key "vectors"
    Contains dataset column metadata
    • vectors Array
      Array of objects with the keys "name" and "array".
• rowAnnotations/columnAnnotations
  Optional array of objects describing additional annotations to join with dataset. [Object]

  • file String
    An xlsx file, a tab-delimited text file, or a gmt file.
  • datasetField String
    Field to match in dataset.
  • fileField String
    Field to match in file.
  • include [String]
    Optional array of fields to include from file.

  Annotate rows matching "name" field in dataset to "id" field in file at https://MY_URL. [{file:"https://MY_URL", datasetField:"name", fileField:"id"}]
• rowSize
  • Number|String (default: 13)
    Heat map row size in pixels or 'fit' to fit heat map to current height.
• width
  • Number
    Total heat map width. If undefined, width will be with of el element.
• columnSize
  • Number|String (default: 13)
    Heat map column size in pixels or 'fit' to fit heat map to current width.
• drawGrid
  • Boolean (default:true)
    Whether to draw heat map grid.
• rowGroupBy/columnGroupBy
  Optional array of metadata names to group the heat map by. [Object]

  • field String
    The metadata field name.

  Group by the type and gender metadata fields

  [{field:"type"}, {field:"gender"}]
• rowFilter/columnFilter
  Optional object that describes filter. Object

  • filters [Object]
    • field String
      The metadata field name.
    • type String
      One of "set", "range", "top", "index"
    • values [String|Number] for "set" filter
      Array of values to include
    • min Number for "range" filter
      Minimum value to include
    • max Number for "range" filter
      Maximum value to include
    • direction String for "top" filter
      One of "top", "bottom", "topAndBottom"
    • n Number for "top" filter
      Number to include
    • indices [Number] for "index" filter
      Array of indices to include
  • isAnd Boolean
    Whether filters are combined by AND or OR.

  Keep rows with annotation "field_1" equal to "A" or "B" and annotation "field_2" between zero and one.

  {isAnd:true, filters:[{type:"set", name:"field_1", values:["A", "B"]}, {type:"range", name:"field_2", min:0, max:1}]}
• colorScheme
  Optional object that describes value to color mappingObject

  • scalingModeString
    "fixed" or "relative" color scheme
  • steppedBoolean
    Whether color scheme is continuous (false) or discrete (true)
  • values[Number]
    Array of values corresponding to colors
  • colorsBoolean
    Array of colors
  • sizeObject
    Optional object that describes the mapping of value to size for an element in the heat map
    • seriesNameString
      Dataset series name to map value to size
    • minNumber
      Minimum value in series used for mapping value to size
    • maxNumber
      Maximum value in series used for mapping value to size
  • transformValuesNumber
    For "fixed" scaling mode: 1 to z-score, 2 to robust z-score
  • conditions[Object]
    Optional array of objects that describe the mapping of value to shape for an element in the heat map
    • seriesNameString
      Dataset series name to map value to a condition
    • colorString
      Shape color
    • shapeString
      Shape name ("circle", "square", "diamond", "triangle-up", "triangle-down", "triangle-left", "triangle-right")
    • inheritColorBoolean
      Whether shape inherits color from color scheme
    • colorString
      Shape color when inheritColor is false
    • v1Number
      Condition one value
    • v2Number
      Condition two value
    • v1OpString
      Condition one operation ("gte", "gt")
    • v2OpNumber
      Condition two operation ("lte", "lt")

  Use a fixed color scheme with color stops at -100, -90, 90, and 100

  { scalingMode : "fixed", stepped : false, values : [ -100, -90, 90, 100], colors : ["#abdda4", "white", "white", "red"]}
• rowSortBy/columnSortBy
  Optional array of sort keys. To sort by an annotation, set "type" to "annotation" and supply a metadata name. To sort by values in the heat map set "type" to "byValues" and set "modelIndices" to an array of model row/column indices in the dataset to sort by. [Object]

  • orderNumber
    0 for ascending, 1 for descending.
  • fieldString
    Annotation field name when sorting by an annotation
  • typeString
    Sort by "annotation" or "byValues"
  • modelIndices[Number]
    Array of model row/column indices in the dataset to sort by when sorting by heat map values

  Sort ascending by gene, and then descending by heat map values in 1st column

  [{field:"gene", order:0, type:"annotation"}, {modelIndices:[0], order:1, type:"byValues"}]
• rowColorModel/columnColorModel
  Describes how annotation values are mapped to colors. The keys in the object are the annotation names. The structure of the object will depend on whether you're specifying a continuous or discrete color map.

  For discrete mappings:

  Map "a" to "red", "b" to "blue", and "c" to "white" for the "type" field.

  {"type":{"a":"red", "b":"blue", "c":"white"}}

  For continuous mappings:

  Map from yellow to green from 0 to 2 for the "score" field.

  {"score":{values:[0, 2], colors:["yellow", "green"]}
• rowShapeModel/columnShapeModel
  Describes how annotation values are mapped to shapes. The keys in the object are the annotation names. The values are one of "circle", "square", "plus", "x", "asterisk", "diamond", "triangle-up", "triangle-down", "triangle-left", "triangle-right", or "circle-minus".

  Map "a" to "diamond", "b" to "asterisk", and "c" to "x" for the "type" field.

  {"type":{"a":"diamond", "b":"asterisk", "c":"x"}}
• rowFontModel/columnFontModel
  Describes how annotation values are mapped to font weights. The keys in the object are the annotation names. The values are one of {"weight":"400"}, {"weight":"700"}, or {"weight":"900"}

  Map "a" to font weight 700

  {"type":{"a":{"weight":"700"}}
• rowDendrogram/columnDendrogram
  • String
    Optional URL to a dendrogram in Newick format
• rowDendrogramField/columnDendrogramField
  • String
    Optional metadata field in dataset to match leaf node ids in the dendrogram Newick file.
• rows/columns
  Optional array of objects describing how to display metadata fields [Object]

  • field String
    Metadata field name
  • display [String]
    "text" to render annotation as text, "color" to render annotation as color, "bar" to render annotation as bar chart, "text_and_font" to encode text using font weight, "text_and_color" to encode text using color.
  • highlightMatchingValues Boolean (default:false)
    Whether to highlight matching values on hover
  • colorByField String
    Optional field name to color this field by.
  • fontField String
    Optional field name to use for mapping values to font weights.
  • min Number
    Optional minimum for bar chart.
  • mid Number
    Optional midpoint for bar chart.
  • max Number
    Optional maximum for bar chart.
  • formatter String
    Optional number format pattern, such as ".4f".

  Display id as text and stdev using text and color

  [{field:"id", display:["text"]}, {field:"stdev", display:["text", "color"]}]
• tools
  Optional array of tools to run at load time [Object]

  [{name:String, params:Object}]

  Cluster rows and columns

  [{ name: "Hierarchical Clustering", params: {cluster: "Rows and columns"} }]