R/flash_plots.R
flash_plot_histogram.RdCreates 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.
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,
...
)An object inheriting from class flash.
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.)
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.
Whether to plot loadings \(L\) or factors \(F\).
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.
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.
A character vector specifying a color for each unique group
specified by pm_groups. Defines the color and fill of the histograms.
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.
Number of bins. Overriden by binwidth. Defaults to 30.
A transparency value between 0 (transparent) and 1 (opaque).
Additional arguments to be passed to
facet_wrap (e.g., nrow or ncol).
A ggplot object.