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Shiny app for making and annotating Volcano plots

Home Page: https://huygens.science.uva.nl/VolcaNoseR/

License: GNU General Public License v3.0

HTML 3.11% R 96.89%

volcano ggplot2 shinyapp shiny proteomics-data-analysis genomic-data-analysis dataviz

volcanoser's Introduction

VolcaNoseR

A Shiny App for making Volcano plots

Running the App

The web-tool runs from a shiny server, and can be accessed at:

o https://huygens.science.uva.nl/VolcaNoseR/

o https://huygens.science.uva.nl/VolcaNoseR2/

o https://amsterdamstudygroup.shinyapps.io/VolcaNoseR/

o https://goedhart.shinyapps.io/VolcaNoseR/, while bandwidth lasts

Alternatively, the app can run from R/Rstudio and this is perhaps the best option for loading large files. See instructions below

Preparations

Note that the app depends on several R packages that need to be installed (shiny, ggplot2, dplyr, magrittr, ggrepel, DT, shinycssloaders, RCurl, readxl).

Run this command in R/Rstudio to download and install all the packages (only needs to be done once):

install.packages("shiny", "tidyverse", "ggrepel", "DT", "shinycssloaders", "RCurl", "readxl", "ggiraph", "htmlwidgets")

o The first option is running it directly from Github. In the command line (in R or Rstudio) type:

shiny::runGitHub('VolcaNoseR', 'JoachimGoedhart')

o The second option is download the app and to use it offline:

-download the app.R and csv files (Data-Vulcano-plot.csv and elife-45916-Cdc42QL_data.csv) with example data.

-Run RStudio and load app.R

-Select 'Run All' (shortcut is command-option-R on a Mac) or click on "Run App" (upper right button on the window)

This should launch a web browser with the Shiny app.

Credits

There are several Shiny apps for Volcano plots that have served as a source of inspiration:

-VolcanoR

-Volcanoshiny

-VolcanoPlot_shiny_app

VolcaNoseR is created and maintained by Joachim Goedhart (@joachimgoedhart)

Example output

Standard output generated with the example data:

Output with user selected annotation of data:

volcanoser's People

Contributors

Stargazers

Watchers

Forkers

animesh genomicsnx amhaslam wardiam eleozzr shinyappstore wangdi2016

volcanoser's Issues

Site wasn't available when downloading iPlot html

It takes multiple tries to download an iPlot html. Error is the the site wasn't available.
https://amsterdamstudygroup.shinyapps.io/VolcaNoseR/
https://goedhart.shinyapps.io/VolcaNoseR/

Flexibility of cut-off values

In the current version sliders are used to set the cut-off values for FC and p-value. There are two issues:
-These sliders have a limited range
-Difficult to set the desired value

Solution: use a nummeric input field that allows users to enter a number.

Decimal separator

Only dots are accepted as decimal separators. Show pop-up to warn users when comma's are used as separators

Plots not loading

Hi Joachim,

Since today i am unable to see any plots in VolcaNoseR. Even when i try to plot the example data i get the following error message:

It happens in chrome as well as microsoft edge.

Hi Joachim,
I am getting a volcano plot but it is inverted: Instead of looking like a V, it looks like an A.
I got normal volcano/V shape doing volcano plots with ggplot2 or EnhancedVolcano with my data set.
Is there any option I should select or unselect?
Also, is there an option to select a specific adjusted p-value?
Thank you very much in advance.
Best,
Etienne

Error: unable to find an inherited method for function ‘select’ for signature ‘"tbl_df

Hello,
When I try to use your shiny app, just using your example data, I get the following error message when I click on the tab 'Plot':
Error: unable to find an inherited method for function ‘select’ for signature ‘"tbl_df"’
Is there anything I can do no my side to fix this?
Thank you very much in advance.
Best, Etienne

Detect file format

Currently, users have to select the filetype that is uploaded (text or excel).
It would save time to detect the file format automatically.

Correct package installation instructions

The app is really useful! The install instructions I used were:
install.packages(c("shiny", "ggplot2", "dplyr", "magrittr", "ggrepel", "DT", "shinycssloaders", "RCurl", "readxl", "ggiraph", "tidyverse"))

I needed the extra packages ggiraph and tidyverse, and needed to pass a vector of package names to the function. The instructions on here didn't work for me.

Website not working

Hello!

I've been using this platform for the last couple of months for my PhD thesis and found it very useful, however, when I attempted to access the site today it wouldn't load. Would you be able to check please?

Thanks,

Margot

colours are gone

Dear Joachim,

The webapp as well as the standalone does not display colours anymore.
edgeR_DLX5_high.txt
attached is the input file.
Am I doing something wrong.
HELP.
regards,
Amit.

Website Down

Continuosly disconnects from server.

Problem to download html file (interactive figure)

When I download html file from iPlot, I have a server error. Inversely, I have no problem when I downloaded a html files from example 1 or 2....

What's happen ?

Thanks