| { | |
| "$schema": "https://vega.github.io/schema/vega-lite/v5.json", | |
| "params": [ | |
| { | |
| "name": "orientation", | |
| "bind": {"input": "checkbox"} | |
| }, | |
| { | |
| "name": "strand", | |
| "value": "true", |
| library("tidyverse") | |
| library("httr") | |
| try_fields <- function(case_hash) { | |
| print(str_c("Now on case with hash:", case_hash, sep=" ") ) | |
| # all fields that can contain a tumor purity value | |
| fields = c( | |
| "files.cases.samples.portions.slides.percent_tumor_cells", | |
| "files.cases.samples.portions.slides.percent_tumor_nuclei", | |
| "samples.portions.slides.percent_tumor_cells", |
Whenever I want to create pull requests to a repo that I don't have write access to, I:
I try to use conda for as many software installations in data analysis as possible, as this will ususally guarantee that I can use up to date versions of that software.
This now includes R, and as I mostly use R through Rstudio Desktop, I checked how I can use a custom R installation with Rstudio Desktop. As described in the Rstudio docs, you just have to set the environment variable RSTUDIO_WHICH_R to the R binary of your wanted installation. For this environment variable to be set when launching Rstudio from Ubuntu's application launcher, you have to make the respective environment setting in the rstudio.desktop file.
As a reminder for me, and maybe as info for others, the general setup is: