R/flash_plots.R
flash_plot_histogram.Rd
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.
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.