Felix Wiegand¹, David Lähnemann¹², Felix Mölder¹³, Hamdiye Uzuner¹, Adrian Prinz¹ Alexander Schramm²⁴, Johannes Köster¹²

¹Bioinformatics and Computational Oncology, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen

²German Cancer Consortium (DKTK). Partner Site University Hospital Essen

³Institute of Pathology, University Medical Center Essen

⁴Laboratory of Molecular Oncology, West German Cancer Center, Department of Medical Oncology, University Hospital Essen

https://koesterlab.github.io

¹ https://shiny.rstudio.com

² https://bioinformaticsworkbook.org

Excel/CSV:

non-interactive
non-visual

Interactive visual document

browser based
portable, server-free
publishable as supplementary file
can handle big data

The problem

The solutions so far

²

Plots:

can only highlight certain aspects

Webservice/R Shiny:

development overhead
not portable (needs server or local deployment)

¹

The datavzrd solution

datasets:
  diffexp:
    path: results/diffexp.csv
    separator: "\t"

  differential_expression:
    dataset: diffexp
    render-table:
      columns:
        accession:
          display-mode: hidden
        name:
          link-to-url: "https://www.genecards.org/{name}"
        type:
          plot:
            heatmap:
              scale: ordinal
              color-scheme: category10
        F:
          plot:
            ticks:
              scale: linear

?

How to communicate derived information

Rapid text based declaration of

datasets (n)
views (m≥n)

Declare

linkouts
heatmaps
tickplots

Define custom plots

for individual table cells
for entire datasets

Jump around between corresponding elements in different views

Export views to

publication-ready figures
Excel

filter rows and display column stats

show and hide row details

Share rows

with mobile devices using QR codes
via mail using data URLs