search

EuracBiomedicalResearch / FamAgg

This is the development version of the FamAgg Bioconductor package.
https://EuracBiomedicalResearch.github.io/FamAgg
MIT License
0 stars 2 forks source link

Output HaploPainter extended pedigree file #13

Closed the-x-at closed 6 years ago

the-x-at commented 6 years ago

Function plotPed with prior call to switchPlotfun("haplopaint") generates a temporary file that is supplied to HaploPainter program. It would be desirable to retrieve this file by some means for manual editing and fine tuning with HaploPainter GUI, e.g. with a new option dev="csv".

the-x-at commented 6 years ago

A nice addon would be a header line as a comment that describes (also tab-separated) each column, as there are many of them. E.g. #FAMID INDIVID DADID MOMID GENDER AFF DEAD SABTOP PROBAND ADOPT TWINS CONSAN TINSYM TBESSYM T1UNDR T2UNDR T3UNDR T4UNDR It is not part of the LINKAGE file format, but HaploPainter explicitly allows comments. Therefore, this information would be helpful when editing the file.

jorainer commented 6 years ago

and what about defining an explicit function export... that saves the info in the haplopainter format?

the-x-at commented 6 years ago

Would that then imply an interface duplication to what can be supplied to plotPed? I am talking about all the fancy parameters like text.beside.symbol, textN.below.symbol, etc. I see them as a nice way to streamline plotting and use HaploPainter GUI only as the very last step for fine tuning.

jorainer commented 6 years ago

You're right. Makes no sense to add all these additional columns to an export call. I like the idea of a device = "csv" - eventually we should also add a device = "dev/null" too :)

jorainer commented 6 years ago

OK, device = "txt" writes the results (including header) to a file and the function returns then the name of that file.

jorainer commented 6 years ago

Fix is in - have a look at it and merge if you're happy @the-x-at

jorainer commented 6 years ago

Done and pushed to Bioconductor. Closing.