DE Test Result

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Differentially Expressed Genes

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Volcano Plot

fGSEA

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GSEA: Hallmark Gene Sets

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Enrichment Summary Plot

Information

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General Information

Self-service interactive tools such as this have great power to support decisions by policy-makers. Shiny applications are a natural fit for this but it is not always easy to share them due to issues including a lack of server space, highly sensitive data and users who aren’t R-savvy.

One approach to this, and which is used in simple dashboard production, is to use interactive HTML widgets based on embeddable JavaScript visualisation libraries. Interactivity in these instances is, however, limited because selections in one widget do not impact the data presented in another.

This example dashboard was generated to demonstrate one approached to these issues: generation of portable HTML-based Shiny-like dashboards generated using the Crosstalk package within RMarkdown outputs. This approach is based on shared data objects that react to user inputs, altering the content of multiple widgets on the fly, and enable easy sharing with stakeholders or collaborators in the form of a static HTML file that can be explored in any standard web browser.

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How to Use

Filters

  • select one or more genes, log2 fold-change directions, or MSigDB Hallmark gene sets from the respective drop down menu on the appropriate page (remove them with your backspace key)
  • drag a slider to adjust the desired value of log2 fold-change, adjusted p-value or normalised enrichment score

Interactive table

  • sort the columns by clicking on the column header
  • scroll through sets of rows by clicking “Next”
  • see how many entries remain after filtering where it says “X - Y of Z rows”

Interactive Plots

  • click and grab to select, drag, zoom and resize the plot area
  • use the toolbar (top-right) to have more finite control over the plot display and export snapshots
  • hover over a marker to reveal a popup with information about that data point

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Tools and Data

R v4.2.1 and RStudio 2022.02.4+500 for macOS were used to build this tool

Packages used for dashboard construction:

The data set used was a bulk mRNA-Seq data set generated by the author (Lewis Quayle, PhD) from quiescent and proliferative sub-populations isolated from the oestrogen-receptor positive MCF-7 human breast cancer cell line and published here