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boxplotr.shiny's Introduction

BoxPlotR

This is the repository for the Shiny application presented in "BoxPlotR: a web tool for generation of box plots" (Spitzer at al. 2014).

Installation

You have two options for running shiny-boxplot:

  1. Launch directly from R and GitHub:
  • Before running the app you will need to have R and RStudio installed (tested with R 3.2.1 and RStudio 0.99.465).

  • Launch the R console

  • Please run these lines in R:

    • install.packages("shiny")
    • install.packages("devtools")
    • devtools::install_github("rstudio/shiny-incubator")
    • install.packages("beeswarm")
    • install.packages("vioplot")
    • install.packages("beanplot")
    • install.packages("RColorBrewer")
  • Then start the app:

    • shiny::runGitHub("BoxPlotR.shiny", "VizWizard")

Your web browser will open the web app.

  1. Install the shiny-server and implement shiny-boxplot as a web application and service:
  • In Ubuntu 12.04+
    • sudo apt-get install gdebi-core
    • wget http://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.0.0.42-amd64.deb (may need to change ubuntu or server version number)
    • sudo gdebi shiny-server-1.0.0.42-amd64.deb
    • edit: /opt/shiny-server/config/default.config in a text editor
      • Change these lines to suit your environment
      • listen SHINY_PORT; (change SHINY_PORT to match the port you want)
      • site_dir SHINY_APP_HOME; (change SHINY_APP_HOME to the location for your shiny apps)
    • make sure SHINY_PORT is open on your firewall
    • Go to your SHINY_APP_HOME
      • cd SHINY_APP_HOME
    • Get the latest shiny-boxplot code from github:
    • Restart shiny-server service:
      • sudo service shiny-server restart

You should now be able to access shiny-boxplot at: http://YOURSITE:**SHINY_PORT**/BoxPlotR.shiny

boxplotr.shiny's People

Contributors

jwildenhain avatar michaelaebi avatar vizwizard avatar

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boxplotr.shiny's Issues

Option to indicate the mean using a bar instead of plus sign

The 'Add sample means' function uses a '+' sign to indicate the mean. This is OK when showing a box plot (given the median is indicated by a bar) but looks weird when showing a dot plot (e.g. for small sample sizes). Would be great if the mean was indicated by a bar instead, or if there was an option to choose either a plus sign or a bar to indicate the mean.

jitter do not work properly

Assuming there 5 same boxplots created in a graph, the data point of the first boxplot with jitter option will still have over-plotting problem. It can be seen that the over plotting problems decrease from one boxplot to another from left to right.

'Save settings'-feature

It would be great to be able to save all settings for a boxplot (separator, titles, axis labels etc.) so that one can easily go back and make changes.

Uncoupling control panel and plot area

Since the control panel can get quite 'long', it would be useful to 'uncouple' the control panel and the plot area so that the plot is always visible.

Option to not display outliers

When displaying data with boxplots, add an option to not show the outliers ("outline=F")

Use case: If there are strong outliers, a user might want to focus on the boxplots and not show any outliers.

Display statistics and selected data points on graph

Implement option to add values of boxplot statistics directly to the plot (median, quartiles). Allow single data points to be shown - not sure how to identify the data point (row number?) and if data points in row number x should be shown in all boxplots if data set has several columns.

Allow longer labels

Longer labels are abruptly cut off toward the left end of the label. Would be great if this was not the case.

Website seems to be broken

Hello @VizWizard thanks for this beautiful software.
I am trying to add new datapoints to my thesis and tried to visualise via the website but whatever I do, I cannot seem to get any visualisations.

I have tried using the "load sample data" option, with default settings to no avail.
I used the website to obtain visualisations as late as third quarter of last year.
I've also tried using the exact same datasets I used last year, but also to no avail.

I've checked through the commit logs and notice some new commits some 18 days ago.

I've done some poking around on the website and see no console errors or even API calls being made.

I would try to follow the instructions on running the project locally, and try to point to earlier commits to see if that solves my issue. Thank you.

Outliers are duplicated when data points are added to plot

When data points are added to the plot (default, bee swarm or jitter), outliers appear twice because they are plotted with the original boxplot and the again when the data points are added.
Solution: When points are to be added, draw box plots with outline=FALSE when adding data points and set ylim = c(min(data), max(data)). Keep in mind orientation of boxplot (ylim vs xlim).

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