Additional project notes go here.
A package that rewrites and expands upon the utility of a collection of functions previously written for PCA plotting and visualizations (prepSpatial.R and PlotPCmaps.R) is to be developed. Additional plotting functions are to be developed (violin plots, scree plots, PC loading plots). Additional utilities are to be added to existing functions (mirroring of PCA plots, axis rotation for PCA plots, hover-over descriptors and IDs for individual points, map inset paired to PCA data).
Data sets we use for illustrating the PCAviz package:
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Iris Data; type
data(iris)in R. -
POPRES data; type
data(popres)in R. -
RegMap data (see the Nature Genetics paper); type
data(regmap)in R.
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"Genes mirror geography" paper and accompanying supplementary materials.
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The rsvd package for randomized singular value decomposition (and PCA) in R.
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New world countries polygons dataset (from mapdata R package) to replace outdated worldpolys.rda dataset.
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Code from preSpatial.R to be modified for new dataset and made into a processing function executed upon loading of the PCAviz library.
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Functions to be updated to match new country polygons:
plotGeoPoints(preSpatial.R),plotPCbiplot(PlotPCmaps.R) andplotPC(PlotPCmaps.R). -
plotPC function to be modified to enable mirroring of PCA plot axes (PlotPCmaps.R).
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Functions from PlotPCmaps.R to be modified to enable the viewing of PCA point details upon hovering over the point, use of Shiny preferred.
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New plotting functions to be developed/integrated: Violin plot, Scree plot and PC loadings plot (Bar plot).