GitLab

Revoked some test changes regarding rhandsontable in mod_table. Added argument to fix columns in rhandsontable in mod_model_panel to make it explicit and remove warning message

Changed filter in selecting ploty points in lod plot to only show unique markers. This works with models of the same phenotype, but may produce implicit errors when multiple models are made for different phenotypes and PVE is of importance. (i.e. showing pve of phenotpye 1 while points for phenotype 2 are selected) Solution could be some method of letting model selection in legend flow through

Added cofactor option to qtlscan and if statements based on checkboxinput for arguments block and cofactor

Added model_list value in rv to collect models accross packages

Added script to work through plotly book where needed

Plot now reacts to selected LG and offspring, changing to selectize and adjusting number of plots accordingly might be interesting. out of bound error does pop up initially after estimation, maybe a system wait or something will resolve this issue

Now possible to select which offspring/LG to show in haplotype visualisation, plot does not adjust yet. Possibly plotly object might be better

Changed IBD page to include more options for estimate_IBD function. importing .rds file possible but not yet function, needs a switch of some sort

Changed SNP dosage input to read.csv(file, row.names = 1) because we expect a matrix as input here with rownames. load_file function doesn't work properly here yet

both rds and csvs can now be used with proper datatableoutput. lists become uneven with mapply used so a switch is needed

Added fileload function so both csv and rds can be imported. Mapply used for options where multiple files can be selected (linkage map).
ouputTable does not show yet though

Now possible to estimate IBDs through heuristic method, has to become more fleshed out to select offspring in haplotype visualisation and linkage group. For HMM the modal spinner may be more effective

Data input fully functional but should be adjusted so user can select right columns for IBD imputation.

IBD imputation moved to its own part but currently not working due to odd formatting while reading in files

Focussing on polyqtlR at the moment for first visualisations and adding functionality to the R Shiny buttons

Added radio buttons for IBD imputation method selection and fileinput for already imputed IBD probabilities

Created R shiny script based on shiny tutorial, which will be customized for the phase 1 development