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Created with Raphaël 2.2.01Mar3Feb28Jan191831Dec825Nov241817159321Oct19186529Sep2827Created first packagemainmainSmall dependency missingAdded dependenciesRefactored code and removed unused files of old app structureMinor changes in selection of points in plotly, removing test tabInput of both polymapr and mappoly object possible and conversion happens immediately. model comparison fully possible, however rescale button happen immediately due to reactivity in the renderNow possible to build a fwd-bwd remim model from qtlpoly using mappoly geno and phenotype data. Not yet in module as new modules are acting up...Added conversion panel with functionality to extract BLUEs from dataframe, need to change to allow for multiple phenotypes stillAdd qtlpoly import optionsSelecting models and chromosomes for plotting now functionalCreate UI for editing plot layout (models to include and chromosome choice)Split up the model panel into separate modules of each modelling and visualisation packagesRevoked 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 messageAdded an editable table for cofactors for the polyqtlR functionadded loading circles for go buttonsChanged 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 throughAdded cofactor option to qtlscan and if statements based on checkboxinput for arguments block and cofactorBasic point selection made possible plotly object, but not persistent yetAdded function options and QTLscan implementationAdded a panel for model building and visualisationAdded parts for plotly visualisationExtended lodmod df to create extra information on tooltipMore testing on plotlyMajor addition of golem style app that has same functionality as previous app.rPlot 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 issueFixed a small change so that all selects start with select_ in rv objectNow possible to select which offspring/LG to show in haplotype visualisation, plot does not adjust yet. Possibly plotly object might be betterChanged IBD page to include more options for estimate_IBD function. importing .rds file possible but not yet function, needs a switch of some sortChanged 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 yetboth rds and csvs can now be used with proper datatableoutput. lists become uneven with mapply used so a switch is neededData table selection for multiple cvs of linkage map worksAdded fileload function so both csv and rds can be imported. Mapply used for options where multiple files can be selected (linkage map).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 effectiveData input fully functional but should be adjusted so user can select right columns for IBD imputation.Add tabs for data tables and made data import functionalEdited readmeRemoved the testing through HTTPSFocussing on polyqtlR at the moment for first visualisations and adding functionality to the R Shiny buttonsAdded a script for testing smaller functions of packagesTesting from surface pro