R/flash_plots.R
flash_plot_structure.Rd
Creates a “structure plot” (stacked bar plot) of posterior means for factors
\(f_{jk}\) or loadings \(\ell_{ik}\). Different “topics” or components
(that is, the different factor/loadings pairs, as specified by kset
)
are represented by different colors. 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 and then stacked (see
ldf.flash
). Note that structure plots were designed for
nonnegative loadings or “memberships”; if posterior means are not
nonnegative then a different type of plot should be used (e.g.,
flash_plot_heatmap
). By default, a 1-d embedding is used to
arrange the rows \(i\) or columns \(j\). This step is usually essential
to creating a readable structure plot; for details, see
structure_plot
.
flash_plot_structure(
fl,
order_by_pve = FALSE,
kset = NULL,
pm_which = c("factors", "loadings"),
pm_subset = NULL,
pm_groups = NULL,
pm_colors = NULL,
gap = 1,
...
)
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.
The colors of the “topics” or components (factor/loadings pairs).
The horizontal spacing between groups. Ignored if pm_groups
is not provided.
Additional parameters to be passed to
structure_plot
.
A ggplot
object.