Okay, think we're finally done with the Rmd. At least it works on my machine!
CN section
manhattan: refactored (plotly was complaining about various things) - I removed the gene colours and instead just use green, think one colour is enough. And also handling sex chromosomes in that one (they were getting filtered out before).
mutCNexprPlot: refactored (again plotly was complaining), also adjusted some column names.
Immunogram section
I don't think it gets evaluated in prod, not sure if we should keep or not. I fixed everything anyway. Not sure what webplot should do.
HRD and Cancer gene section
Refactored, working now.
Drug section
Replaced the rapportools::is.empty function with a simple is.na which should do for the majority of cases. Those chunks don't even get evaluated.
We need to update the CIViC files at some stage (not now); URLs it uses are outdated and point to insecure links.
Addendum section
(Yes, reached the addendum!)
Refactored to display the info in better looking tables
Okay, think we're finally done with the Rmd. At least it works on my machine!
CN section
manhattan: refactored (plotly was complaining about various things) - I removed the gene colours and instead just use green, think one colour is enough. And also handling sex chromosomes in that one (they were getting filtered out before).mutCNexprPlot: refactored (again plotly was complaining), also adjusted some column names.Immunogram section
webplotshould do.HRD and Cancer gene section
Drug section
rapportools::is.emptyfunction with a simpleis.nawhich should do for the majority of cases. Those chunks don't even get evaluated.Addendum section
(Yes, reached the addendum!)