plot.flash: Plot flash object
In stephenslab/flashr: Empirical Bayes Matrix Factorization

plot.flash

R Documentation

Plot flash object

Description

plot method for class 'flash'.

Usage

## S3 method for class 'flash'
plot(x, plot_scree = TRUE, plot_factors = FALSE,
  factor_kset = 1:x$nfactors, factor_colors = NULL,
  factor_legend_size = 5, plot_loadings = FALSE,
  loading_kset = 1:x$nfactors, loading_colors = NULL,
  loading_legend_size = 5, plot_grid_nrow = 2, plot_grid_ncol = 2,
  ask = (plot_factors || plot_loadings) && dev.interactive(), ...)

Arguments

`x`	Flash object to plot.
`plot_scree`	Whether to include a scree plot of the proportion of variance explained per factor/loading pair.
`plot_factors`	Whether to plot the factors indexed by `kset`.
`factor_kset`	If `plot_factors` is `TRUE`, then `factor_kset` specifies which factors will be plotted. Defaults to all factors.
`factor_colors`	If `plot_factors` is `TRUE`, then `factor_colors` specifies the colors to be used for the factor variables. If colors are used, then a legend will be shown alongside the factor plots.
`factor_legend_size`	If `factor_colors` is not `NULL`, then `factor_legend_size` specifies the size of the legend show alongside the factor plots.
`plot_loadings`	Whether to plot the loadings indexed by `kset`.
`loading_kset`	If `plot_loadings` is `TRUE`, then `loading_kset` specifies which loadings will be plotted. Defaults to all loadings.
`loading_colors`	If `plot_loadings` is `TRUE`, then `loading_colors` specifies the colors to be used for the loading variables. If colors are used, then a legend will be shown alongside the loading plots.
`loading_legend_size`	If `loading_colors` is not `NULL`, then `loading_legend_size` specifies the size of the legend show alongside the loading plots.
`plot_grid_nrow`	The number of rows to use when displaying multiple factor/loading plots on a single screen.
`plot_grid_ncol`	The number of columns to use when displaying multiple factor/loading plots on a single screen.
`ask`	Should the user be prompted before displaying each successive plot?
`...`	Additional arguments (not used by this method).