#html #visual #config-file #report #user #tools #reports #create #collections #customization

app datavzrd

A tool to create visual HTML reports from collections of CSV/TSV tables

66 stable releases

Uses new Rust 2021

new 2.14.1 Jan 23, 2023
2.11.1 Dec 20, 2022
2.10.0 Nov 30, 2022
1.19.0 Aug 24, 2022
0.3.0 Feb 18, 2022

#3 in Visualization

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MIT license

1.5MB
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datavzrd

A tool to create visual and interactive HTML reports from collections of CSV/TSV tables. Reports include automatically generated vega-lite histograms per column. Plots can be fully customized by users via a config file. These also allow the user to add linkouts to other websites or link between multiple tables. An example report can be viewed online with the corresponding config file.

Usage

datavzrd config.yaml --output results/

Configuring datavzrd

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: My beautiful datvzrd report
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:
  table-a:
    dataset: table-a
    desc: |
      # A header
      This is the **description** for *table-a*.
    render-table:
      columns:
        x:
          custom: |
            function(value, row) {
              // Access cell value or any other value of the same row (by row.<colname>)
              // to render custom content.
              return `<b>${value}</b>`;
            }
        y:
          link-to-url: 'https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g={value}'
  table-b:
    dataset: table-b
    render-table:
      columns:
        significance:
          optional: true
          custom-plot:
            data: |
              function(value, row) {
                // Generate data for this cell, having access to the value and any other values from
                // the same row.
                return [{"significance": value, "threshold": value > 60}]
              }
            spec: |
              {
                "$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}}
              }
  gene-mycn:
    dataset: gene-mycn
    page-size: 40
    render-table:
      columns:
        frequency:
          plot:
            ticks:
              scale: linear
        quality:
          plot:
            heatmap:
              scale: linear
              range:
                - green
                - red
  gene-mycn-plot:
    dataset: gene-mycn
    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}}
        }

name

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

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.

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 1000 rows.

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.

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

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.
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 100
render-table Configuration of individual column rendering
render-plot Configuration of a single plot
render-html Configuration of a custom html 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

render-table

render-table contains definitions for a table view

keyword explanation
columns Configuration of columns
headers Configuration of the additional 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), or a regular expression (e.g. regex('prob:.+') for matching all columns starting with prob:):

keyword explanation default possible values
link-to-url Renders a link to the given url with {value} replace 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).
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
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

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.

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.

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

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

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

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

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.

heatmap

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

keyword explanation default
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
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.

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.

Authors

Dependencies

~14MB
~268K SLoC