Claire Petry Agenda Objectives of the app Demo How to upload your - - PowerPoint PPT Presentation

explort R Shiny App

October 10th 2017

Claire Petry

Agenda

• Objectives of the app
• Demo

– How to upload your data (CSV or FIT file) – How to create plots – How to export R code and use it

• Next steps
• Conclusion

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Objectives of the app

• Interactive data exploration: create and customize basic plots to

– Review data – Identify potential data issues – Identify outliers – …

• Export R code to

– Be able to recreate the plots of interest – Allow R beginners to use it as a kind of template, to create plots and personnalize them without starting from scratch

• Spotfire also allows the interactive data exploration, but not the reproducibility and traceability of

the plots

Explore Export explort

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Demo

• Prerequisite to run the app

No data manipulation done by the app (except subsetting) the data file must be ready to use (create categorical variables with the right labels etc.)

• Demo video

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Demo - How to upload a CSV file

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Demo - How to upload a FIT file

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Demo - How to create plots

• 5 types of plots can be created and customized via the app

– Scatter plots – Spaghetti plots – Boxplots – Diagnostic plots – Mean plots

• To create one of those plots, click on the corresponding tab in the menu bar

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Demo - How to create plots

• Available features for each type of plots

Scatter plots Spaghetti plots Boxplot s Diagnostic plots Mean plots X and Y variables

• Color / shape variables
• Facetting variable(s)
• Y scale (normal or log)
• Dose normalization
• Plot title and labels
• Legend position
• Identity line
• Smooth line
• Mean / median line
• Interactivity
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Demo - How to export R code

• In the tabs to create plots, select the plots of interest by clicking on ‘‘Add to selection’’
• In the Main tab, once all the plots of interest have been selected:

– select the desired extension for the file that will be created running the exported R code (either .docx or .pdf) – export the corresponding R code by clicking on ‘‘Export code’’

• The exported code will be saved in your Downloads folder

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Demo - How to use the exported R code

• Open the R program which has been created and adapt it

– Change the path of the uploaded data file – Define the path of the .docx or .pdf file that will be created running the R code – Modify the code if necessary: change titles, labels… – Add comments to make your program readable

• Run your updated R program and

get your plots in the defined format

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Next steps

• Update the R script template to warn users about required edits (input/output files)
• Update the diagnostic plots display and add other diagnostic plots (distribution of model

parameters)

• Identify and correct bugs
• Get users’ feedback
• Improve the app

– Integrate other types of plots (histograms, bar plots…) – Add more interactivity – Improve performance of the app

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Conclusion

• explort allows interactive data exploration

– Creation of different types of data visualizations – Customization of the plots via many features – Detection of outliers – Display of selected data in a table below the plot

• It is also designed to export the R code to reproduce the plots of interest

– Ready to run code – Can be used as a template to create and customize additional plots – The user can choose the format of the file that will be created running the exported code – Does not require any programming skills – Guaranties the traceability and reproducibility of the plots

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Thank you

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Back-up

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Demo - How to create plots

• Scatter plot example

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Demo - How to create plots

• Spaghetti plot example

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Demo - How to create plots

• Boxplot example

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Demo - How to create plots

• Diagnostic plots example

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Demo - How to create plots

• Mean plot example

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Doing now what patients need next

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