Configuration

Datavzrd allows the user to easily customize it’s interactive HTML report via a config file. When generating large reports, templating yaml files can be a bit tricky. We advise using yte for easy yaml templating with python expressions.

name

name allows the user to optionally set a name for the generated report that will be heading all resulting tables and plots.

Example:

name: "my report"

default-view

default-view allows the user to optionally specify a view for the generated report that will be shown when opening the index file.

Example:

default-view: "gene-overview"

max-in-memory-rows

max-in-memory-rows defines the threshold for the maximum number of rows in memory. If the given dataset exceeds the threshold the data will be split across multiple pages and their html files. Defaults to 20000 rows.

Example:

max-in-memory-rows: 5000

aux-libraries

aux-libraries allows to add one or more js libraries via cdn links for usage in render-html. The keyword expects a list of urls that link to the js libraries.

Example:

aux-libraries:
    - "https://cdn.jsdelivr.net/npm/mathjs@13.0.2/lib/browser/math.min.js"
    - "https://cdn.jsdelivr.net/npm/fraction.js@4.3.7/fraction.min.js"

webview-controls

webview-controls allows to turn on sharing individual rows via a link with the data encoded into a url pointing to a webview that hosts a static version of datavzrd at https://datavzrd.github.io. Note that when using the link the row data can temporarily occur (in base64-encoded form) in the server logs of the given webview host. Defaults to false.

Example:

webview-controls: true

datasets

datasets defines the different datasets of the report. This is also the place to define links between your individual datasets.

keyword	explanation	default
path	The path of the CSV/TSV file
separator	The delimiter of the file	,
headers	Number of header rows in the file	1
links	Configuration linking between items
offer-excel	Whether to offer the dataset as an excel worksheet.	false

Example:

datasets:
    table-a:
        path: "table-a.csv"
        links:
            gene details:
                column: gene
                view: "gene-{value}"
            gene expression:
                column: gene
                table-row: table-b/gene
                optional: true
    table-b:
        path: table-b.csv
        separator: ;
    gene-mycn:
        path: "genes/table-mycn.csv"
        headers: 2
        links:
            some expression:
                column: quality
                view: table-b

views

views consists of all different CSV/TSV views (table or plot) that should be included in the resulting report. If neither render-table nor render-plot is present, datavzrd will render the given file as a table. Each item definition can contain these values:

keyword	explanation	default
desc	A description that will be shown in the report. Markdown is allowed and will be rendered to proper HTML. It is also possible to add latex formulas with `latex ... `.
dataset	The name of the corresponding dataset to this view defined in datasets
datasets	Key-value pairs to include multiple datasets into a render-plot configuration. Key must be the name of the dataset in the given vega-lite specswhile the value needs to be the name of a dataset defined in datasets.
page-size	Number of rows per page	20
render-table	Configuration of individual column rendering
render-plot	Configuration of a single plot
render-html	Configuration of a custom html view
render-img	Configuration of an image view
hidden	Whether or not the view is shown in the menu navigation	false
max-in-memory-rows	Overwrites the global settings for max-in-memory-rows
spell	Uses a datavzrd spell to configure a view. Any other defitions for the view will be overwritten by the spell.

Example:

views:
    table-a:
        dataset: table-a
        desc: "This is the **description** for *table-a*. Markdown is allowed!"
        render-table: ...

render-table

render-table contains definitions for a table view

keyword	explanation
columns	Configuration of columns
add-columns	Configuration of additionally generated columns
headers	Configuration of the additional headers

Example:

render-table:
    columns:
        ...
    add-columns:
        ...
    headers:
        ...

columns

columns contains individual configurations for each column that can either be adressed by its name defined in the header of the CSV/TSV file, its 0-based index (e.g. index(5) for the 6th column), a range expression (e.g. range(5, 10) for the 5th column to 9th column) or a regular expression (e.g. "regex('prob:.+')" for matching all columns starting with prob:):

keyword	explanation	default	possible values
link-to-url	You can either specify only a single url or key value pairs with a name as the key and the url as the value that will then be accessible via a dropdown. Use the special keyword `custom-content` to change the title of the link or the dropdown with a javascript function looking like this: `function my_link_title(value, row) { return 'Open link to ' + value }`
custom	Applies the given js function to render column content. The parameters of the function are similar to the ones defined here
label	Allows to specify a label that will be used in the table header instead of the column title in the given dataset.
custom-path	Allows to specify a path to a file that contains a js function similar to custom. The file should only contain one js function (the name of the function shouldn’t matter) and should look like this. The given path is relative to the directory you are currently in and running datavzrd from.
custom-plot	Renders a custom vega-lite plot to the corresponding table cell
plot	Renders a vega-lite plot defined with plot to the corresponding table cell
ellipsis	Shortens values to the first n given characters with the rest hidden behind a popover. With n = 0 the cell will be empty and the value will only be shown in a popover.
optional	Allows to have a column specified in render-table that is actually not present.	false	true, false
display-mode	Allows to hide columns from views by setting this to `hidden` or have a column only in detail view by setting this to `detail`.	normal	detail, normal, hidden
precision	Allows to specify the precision of floats. It expects an integer specifying the decimal places that will be shown. Values smaller than $1 / (10^{precision})$ will be displayed in scientific notation with the same number of decimal places.	2
plot-view-legend	Specifies whether the column in the plot-view should include a legend or not.	false	true, false
spell	Uses a datavzrd spell to configure the column. Any other defitions for the column will be overwritten by the spell.

Example:

columns:
    age:
        display-mode: detail
    impact:
        plot:
            ...
        optional: true

add-columns

add-columns allows to generate new columns out of the existing dataset.

keyword	explanation	default	possible values
value	A javascript function taking a row of the dataset as the parameter that returns the value for the newly generated column. A value named `age` may be accessed in the function via `function my_new_col(row) { return row.age * 2 }` for example.
link-to-url	You can either specify only a single url or key value pairs with a name as the key and the url as the value that will then be accessible via a dropdown. Use the special keyword `custom-content` to change the title of the link or the dropdown with a javascript function looking like this: `function my_link_title(value, row) { return 'Open link to ' + value }`
custom-plot	Renders a custom vega-lite plot to the corresponding table cell
display-mode	Allows to hide columns from views by setting this to `hidden` or have a column only in detail view by setting this to `detail`.	normal	detail, normal, hidden

Example:

add-columns:
    my-new-column:
        value: function(value) { return value + 3 }

headers

headers contains definitions for additional header rows. Each row can be accessed with its index starting at 1 (0 is the first header row that can’t be customized).

keyword	explanation
label	Allows to add an additional label to the corresponding header
plot	Renders a vega-lite plot defined with plot to the corresponding table cell (currently only the heatmap type is supported in header rows)
display-mode	Allows to hide the header row by setting this to `hidden`.
ellipsis	Shortens values to the first n given characters with the rest hidden behind a popover. With n = 0 the cell will be empty and the value will only be shown in a popover.

Example:

headers:
    1:
        ellipsis: 10

render-plot

render-plot contains individual configurations for generating a single plot from the given CSV/TSV file.

keyword	explanation
spec	A schema for a vega lite plot that will be rendered to a single view
spec-path	The path to a file containing a schema for a vega lite plot that will be rendered to a single view. The given path is relative to the directory you are currently in and running datavzrd from.

Example:

render-plot:
    spec: |
        {
            "$schema": "https://vega.github.io/schema/vega-lite/v5.json",
            "mark": "circle",
            "encoding": {
             "size": {"field": "significance", "type": "quantitative", "scale": {"domain": [0,100]}},
             "color": {"field": "threshold", "scale": {"domain": [true,false]}},
             "href": {"field": "some expression"}
            },
            "config": {"legend": {"disable": true}}
        }

render-html

render-html contains individual configurations for generating a single custom view where a global variable data with the dataset in json format can be accessed in the given js file. The rendered view contains a <div id="canvas"> that can then be manipulated with the given script. By default, the div uses the full width and centers its contents. Of course, the divs CSS can be overwritten via Javascript. jQuery is already available, any other necessary Javascript libraries can be loaded via aux-libraries.

keyword	explanation
script-path	A path to a js file that has access to the dataset and can manipulate the given canvas of the rendered view

Example:

render-html:
    script-path: "scripts/my-page.js"

render-img

render-img allows confiuring a datvazrd view displaying a simple png or svg image.

keyword	explanation
path	A path to the image file that shall berendered into the resulting view

Example:

render-img:
    path: "resources/my-plot.png"

links

links can configure linkouts between multiple items.

keyword	explanation	default
column	The column that contains the value used for the linkout
table-row	Renders as a linkout to the other table highlighting the row in which the gene column has the same value as here
view	Renders as a link to the given view
optional	Allows missing values in linked tables	false

Check datasets for an example use case.

custom-plot

custom-plot allows the rendering of customized vega-lite plots per cell.

keyword	explanation	default
data	A function to return the data needed for the schema (see below) from the content of the column cell
spec	The vega-lite spec for a vega plot that is rendered into each cell of this column
spec-path	The path to a file containing a schema for a vega-lite plot that is rendered into each cell of this column
vega-controls	Whether or not the resulting vega-lite plot is supposed to have action-links in the embedded view	false

Example:

custom-plot:
    data: |
        function(value, row) {
            // Generate data for this cell, having access to the value and any other values from the same row.
            return [{"significance": value, "threshold": value > 60}]
        }
    spec: |
        {
            "$schema": "https://vega.github.io/schema/vega-lite/v5.json",
            "mark": "circle",
            "encoding": {
            "size": {"field": "significance", "type": "quantitative", "scale": {"domain": [0,100]}},
            "color": {"field": "threshold", "scale": {"domain": [true,false]}}
            },
            "config": {"legend": {"disable": true}}
        }

link-to-url

link-to-url allows rendering a link to a given url with {value} replaced by the value of the table. Multiple links will result in a dropdown menu.

keyword	explanation	default
url	The url where {value} is replaced by the value of the table. Other values of the same row can be accessed by their column header (e.g. {age} for a column named age).
new-window	Whether or not the rendered link will be opened in a new window or not	true

It is also possible to use custom-content to change the content of the dropdown button.

Example:

link-to-url:
    custom-content: function(value, row) { return `Find out more about ${value}`; }
    Wikipedia:
            url: "https://de.wikipedia.org/wiki/{value}"
    Letterboxd:
            url: "https://letterboxd.com/search/{value}"
            new-window: false

plot

plot allows the rendering of either a tick-plot for numeric values or a heatmap for nominal values.

keyword	explanation
ticks	Defines a tick-plot for numeric values
heatmap	Defines a heatmap for numeric or nominal values
bars	Defines a bar-plot for numeric values

Example:

plot:
    heatmap:

ticks

ticks defines the attributes of a tick-plot for numeric values.

keyword	explanation
scale	Defines the scale of the tick plot
domain	Defines the domain of the tick plot. If not present datavzrd will automatically use the minimum and maximum values for the domain
aux-domain-columns	Allows to specify a list of other columns that will be additionally used to determine the domain of the tick plot. Regular expression (e.g. `"regex('prob:.+')"` for matching all columns starting with `prob:`) are also supported as well as range expressions (e.g. `range(5, 10)` for the 5th column to 9th column).
color	Defines the color of the tick plot

Example:

plot:
    ticks:
        domain:
            - 10
            - 50
        scale: log

heatmap

heatmap defines the attributes of a heatmap for numeric or nominal values.

keyword	explanation	default
type	Corresponds to the type definition of vega-lite. Either `nominal`, `ordinal` or `quantitative`. This overrides any given scale and color-scheme/range configuration and provides a quick way to setup any heatmap configuration. Using `nominal` or `ordinal` results in an ordinal scale with the color-scheme `category20` while `quantitative` results in a linear scale using the `blues` scheme.
scale	Defines the scale of the heatmap
color-scheme	Defines the color-scheme of the heatmap for nominal values
range	Defines the color range of the heatmap as a list
domain	Defines the domain of the heatmap as a list
domain-mid	Allows defining the mid point of a given numeric domain. If a domain is specified it must be of length 2, otherwise datavzrd will automatically set the outer domain from the given column of the dataset. The given color range array must be of length 3 where the middle entry corresponds to the domain-mid value.
clamp	Defines whether values exceeding the given domain for continuous scales will be clamped to the minimum or maximum value.	true
aux-domain-columns	Allows to specify a list of other columns that will be additionally used to determine the domain of the heatmap. Regular expression (e.g. `"regex('prob:.+')"` for matching all columns starting with `prob:`) are also supported.
custom-content	Allows to render custom content into any heatmap cell (while using the actual cell content for the heatmap color). Requires a `function(value, row)` that returns the text value that will be displayed in the cell.

Example:

plot:
    heatmap:
        scale: ordinal
        color-scheme: category20

bars

bars defines the attributes of a bar-plot for numeric values.

keyword	explanation
scale	Defines the scale of the bar plot
domain	Defines the domain of the bar plot. If not present datavzrd will automatically use the minimum and maximum values for the domain
aux-domain-columns	Allows to specify a list of other columns that will be additionally used to determine the domain of the bar plot. Regular expression (e.g. `"regex('prob:.+')"` for matching all columns starting with `prob:`) are also supported.
color	Defines the color of the bar plot

Example:

plot:
    bars:
        scale: linear
        domain:
            - 1
            - 10
        color:
            scale: linear
            range:
                - red
                - green

color

color defines the attributes of a color scale definition for tick and bar plots

keyword	explanation
scale	Defines the scale of the tick or bar plot
domain	Defines the domain of the color scale of the tick or bar plot. If not present datavzrd will automatically use the minimum and maximum values for the domain
domain-mid	Defines a mid point of the domain. The argument is passed on straight to the vega-lite domain defintion
range	Defines the color range of the tick or bar plot as a list

Example:

color:
    scale: linear
    range:
        - red
        - green

spell

spell simplify the process of creating reports by allowing users to define common configurations in a modular way.

keyword	explanation
url	Specifies the spell to use. This can be any local file path, specific versioned URLs (e.g. `v1.0.0/stats/p-value`), or any remote URL like `https://github.com/datavzrd/datavzrd-spells/raw/main/stats/p-value/spell.yaml`
with	Defines the parameters passed to the spell.

Example:

render-table:
  columns:
    p-value:
      spell:
        url: "v1.0.0/stats/p-value"
        with:
          significance_threshold: 0.05