flash_plot_histogram: Create histograms of factors or loadings for a flash fit
In willwerscheid/flashier: Empirical Bayes Matrix Factorization

flash_plot_histogram

R Documentation

Create histograms of factors or loadings for a flash fit

Description

Creates a histogram or sequence of histograms of posterior means for factors f_{jk} or loadings \ell_{ik}. One plot is created for each value of k in kset. Values are normalized so that the maximum absolute value for each factor f_{\cdot k} or set of loadings \ell_{\cdot k} is equal to 1 (see ldf.flash). If pm_groups is specified, then overlapping semi-transparent histograms are created, with one histogram per group specified by pm_groups. This option works best when the number of groups is small or when groups are well separated across components.

Usage

flash_plot_histogram(
  fl,
  order_by_pve = FALSE,
  kset = NULL,
  pm_which = c("factors", "loadings"),
  pm_subset = NULL,
  pm_groups = NULL,
  pm_colors = NULL,
  binwidth = NULL,
  bins = NULL,
  alpha = 0.5,
  ...
)

Arguments

`fl`	An object inheriting from class `flash`.
`order_by_pve`	If `order_by_pve = TRUE`, then factor/loadings pairs will be ordered according to proportion of variance explained, from highest to lowest. (By default, they are plotted in the same order as `kset`; or, if `kset` is `NULL`, then they are plotted in the same order as they are found in `fl`.)
`kset`	A vector of integers specifying the factor/loadings pairs to be plotted. If `order_by_pve = FALSE`, then `kset` also specifies the order in which they are to be plotted.
`pm_which`	Whether to plot loadings `L` or factors `F`.
`pm_subset`	A vector of row indices `i` or column indices `j` (depending on the argument to `pm_which`) specifying which values `\ell_{i \cdot}` or `f_{j \cdot}` are to be shown. If the dataset has row or column names, then names rather than indices may be specified. If `pm_subset = NULL`, then all values will be plotted.
`pm_groups`	A vector specifying the group to which each row of the data `y_{i \cdot}` or column `y_{\cdot j}` belongs (groups may be numeric indices or strings). A group must be provided for each plotted row `i` or column `j`, so that the length of `pm_groups` is exactly equal to the number of rows or columns in the full dataset or, if `pm_subset` is specified, in the subsetted dataset.
`pm_colors`	A character vector specifying a color for each unique group specified by `pm_groups`. Defines the color and fill of the histograms.
`binwidth`	The width of the bins (a numeric value). The default is to use the number of bins in `bins`, covering the range of the data.
`bins`	Number of bins. Overriden by `binwidth`. Defaults to 30.
`alpha`	A transparency value between 0 (transparent) and 1 (opaque).
`...`	Additional arguments to be passed to `facet_wrap` (e.g., `nrow` or `ncol`).