kasperskytte/amplicon-visualiser

A shiny app to visualise amplicon data, based on ampvis2

Amplicon-visualiser

A shiny app to visualise amplicon data based on the ampvis2 package (https://github.com/MadsAlbertsen/ampvis2).

Live at https://kasperskytte.shinyapps.io/shinyampvis/

Run in RStudio (as administrator) on your local computer for larger data sets:

install.packages("shiny")
shiny::runGitHub("amplicon-visualiser","kasperskytte")

This will install all the required packages as well as launch the app. If you still get the error "there is no package 'packagename'" then just use install.packages("packagename") to install the required package(s).

amplicon-visualiser's Issues

Error in Alpha diversity plot

After installing all the packages manually I could launch the server, all works so far, but the alpa diversity plot gives an error:

Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
The following sample(s) have not been rarefied (less than 44326 reads):
16SAMP-747, 16S-AMP-1168, 16SAMP-4603, 16S-AMP-1149, 16SAMP-537, 16S-AMP-1114, 16SAMP-3893, 16SAMP-703, 16SAMP-638, 16SAMP-2611, 16S-AMP-1100, 16SAMP-608, 16SAMP-636, 16SAMP-13288, 16SAMP-719, 16S-AMP-1098, 16SAMP-536, 16S-AMP-1169, 16SAMP-635, 16SAMP-637, 16SAMP-717, 16S-AMP-1148, 16SAMP-735, 16SAMP-729, 16SAMP-738, 16SAMP-2613, 16SAMP-10925, 16SAMP-3913, 16SAMP-716, 16SAMP-726, 16SAMP-728, 16SAMP-625, 16SAMP-736, 16SAMP-13281, 16SAMP-626, 16SAMP-704, 16SAMP-2612, 16SAMP-746, 16SAMP-522, 16SAMP-516, 16S-AMP-1170, 16S-AMP-1099, 16SAMP-10932, 16SAMP-740, 16SAMP-739, 16SAMP-4597, 16SAMP-535, 16SAMP-3941, 16SAMP-3953, 16SAMP-720, 16SAMP-705, 16SAMP-10907, 16SAMP-538, 16SAMP-10911, 16SAMP-737, 16SAMP-4591, 16SAMP-745, 16SAMP-706, 16SAMP-3946, 16S-AMP-1101, 16SAMP-10896, 16SAMP-748, 16SAMP-725, 16SAMP-730, 16S-AMP-1107, 16SAMP-727
Warning: Error in %>%: no function to return from, jumping to top level
  175: tidyr::gather
  174: dplyr::filter
  173: mutate
  172: ggplot
  170: renderPlot
  168: func
  128: drawPlot
  114: <reactive:plotObj>
   98: drawReactive
   85: renderFunc
   84: output$alphadiv_plot
    3: runApp
    2: runUrl
    1: shiny::runGitHub

I think maybe the tidyr::gather package is the problem, any idea if a specific version should be used ?

Packages not installed when launching

I tried to run it locally:
Rscript -e "shiny::runGitHub('amplicon-visualiser','kasperskytte')"

But get this error when accessing the url:

Downloading https://github.com/kasperskytte/amplicon-visualiser/archive/HEAD.tar.gz
Loading required package: shiny

Listening on http://127.0.0.1:5796
Warning: Error in library: there is no package called ‘DT’
  66: <Anonymous>
  65: stop
  64: library
   3: runApp
   2: runUrl
   1: shiny::runGitHub
Warning: Error in library: there is no package called ‘DT’
  66: <Anonymous>
  65: stop
  64: library
   3: runApp
   2: runUrl
   1: shiny::runGitHub
Warning: Error in library: there is no package called ‘DT’
  66: <Anonymous>
  65: stop
  64: library
   3: runApp
   2: runUrl
   1: shiny::runGitHub
Warning: Error in library: there is no package called ‘DT’
  66: <Anonymous>
  65: stop
  64: library
   3: runApp
   2: runUrl
   1: shiny::runGitHub
^C

Execution halted