medvir/shiny-server

A collection of Shiny Apps hosted on our shiny server. The apps can be accessed by browser within the UZH network.

shiny-server's Issues

pdf export of rainbow_tree looks different than in shiny app

The pdf export of rainbow_tree looks different than in shiny app (distorted, different font size, etc.).
Ideally, export would look exactly like screen. Change settings of export?

Shiny servers disconnects when uploading large xlsx files to DIA Statistik

What I tried so far:

• large (80'000 rows) xlsx fails
• large (80'000 rows) csv works fine
• small (100 rows) xlsx works
• large xlsx (80'000 rows) with only two column works

VirMetRunAnalysis species table limit of 100 entries

The species table of the shiny-server/NGS/VirMetRunAnalysis/ app has a limit of 100 entries. If there are more, they are not displayed.

This limit could be increased here:

shiny-server/NGS/VirMetRunAnalysis/server.R

Line 123 in fc46ba2

options = list(pageLength = 100,

The reason for this limit and not allowing for a paged table is, that the second table (Corresponding virus reference sequences) won't work properly if you're on the second page.

In my opinion nothing to fix but to remember that there's this limitation.

VirMetResults improvements

• make window for selecting samples bigger
• include fungi in taxonomic overview

VirMetRunAnalysis fails to create a proper report if sample-name is not as expected

We currently expect the sample name to contain a 10-digit number, sample type and DNA/RNA for the two workflows.
Certain parts of the report might not work properly if any of these information is missing.

We'll maybe fix this at some point, but has not a very high priority I guess.

Adapt VirMet Run Analysis to work with new VirMet orgs_species_found.tsv file

During the last VirMet update, the layout of the orgs_species_found.tsv file changed a bit. It now contains additional infos which somehow fails the current shiny app.

We could now
a) fix it so it'll accept both old and new orgs_species_found.tsv files
b) look forward and change it so it's optimized for the new output

Add filter in VirMetAnalysis to hide phages.

Don't show any reads that align to sequences that contain "phage" in the name.
Filter should be able to be turned on/off in shiny app.

shiny server login only possible for @miuber

Only mihuber has access to the shiny server, because it uses his key. This should be changed to a common key that other people from the group can as well access the shiny server and publish apps.

VirMetAnalysis shows NA instead of 0 in report

VirMetAnalysis shows NA instead of 0 in report

VirMetRunAnalysis read length for coverage score is hardcoded to 151

VirMetRunAnalysis read length for coverage score is hardcoded to 151 in server.R.
mutate(covered_exp = 100 * (1 - exp(-reads * 151 / seq_len)))
Maybe we could add a shiny input field to change this if we analyse external datasets with different read lengths. Default should stay 151.

Generation of pdf reports not working.

Problem of markdown and/or latex.

Package tidyverse not installing/loading on shiny server

At the moment, one has to use the individual packages (dplyr, tidyr, readr, ggplot2).