A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
Estimate breeding values - Adapted function from QTLpoly
Calculates homologues probabilities - Adapted from MAPpoly
Viewmap object sanity check
Viewpoly object sanity check
viewqtl object sanity check
Change ggplot coordinates to plot radar - From package see
Get effects information
Returns the class with the highest probability in a genotype probabili...
Draws linkage map, parents haplotypes and marker doses Adapted from MA...
Filter non-conforming classes in F1, non double reduced population. Fu...
Extract the LOD Scores in a 'mappoly.map' object Function from MAPpo...
Color pallet ggplot-like - Adapted from MAPpoly
Map functions - from MAPpoly
Import data from polymapR
Import phased map list from polymapR
Is it a probability dataset? Function from MAPpoly.
Gets summary information from map. Adapted from MAPpoly
Haldane map function. From MAPpoly
Chi-square test. Function from MAPpoly.
Only the plot part of plot_profile function
Linkage phase format conversion: list to matrix. Function from MAPpoly...
Linkage phase format conversion: matrix to list. Function from MAPpoly...
Plots mappoly.homoprob from MAPpoly
Scatter plot relating linkage map and genomic positions
Plot effects data
Plot a genetic map - Adapted from MAPpoly
Plot a single linkage group with no phase - from MAPpoly
Logarithm of P-value (LOP) profile plots. Modified version of QTLp...
Converts diaQTL output to viewqtl object
Upload example files
Upload hidecan example files
prepare maps for plot - from MAPpoly
Converts map information in custom format files to viewmap object
Converts list of mappoly.map object into viewmap object
Converts polymapR ouputs to viewmap object
Converts polyqtlR outputs to viewqtl object
Converts QTL information in custom files to viewqtl object
Converts QTLpoly outputs to viewqtl object
Check hidecan inputs
Run the Shiny Application
Polysomic segregation frequency - Function from MAPpoly
Plot selected haplotypes
Summary maps - adapted from MAPpoly
Provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.