plot.flash: Plot method for flash objects
In willwerscheid/flashier: Empirical Bayes Matrix Factorization

plot.flash

R Documentation

Plot method for flash objects

Description

Plots a flash object. Several types of plot are possible: see parameter plot_type below as well as functions flash_plot_scree, flash_plot_bar, flash_plot_heatmap, flash_plot_histogram, flash_plot_scatter, and flash_plot_structure.

Usage

## S3 method for class 'flash'
plot(
  x,
  include_scree = TRUE,
  include_pm = TRUE,
  order_by_pve = FALSE,
  kset = NULL,
  pm_which = c("factors", "loadings"),
  pm_subset = NULL,
  pm_groups = NULL,
  pm_colors = NULL,
  plot_type = c("scree", "bar", "heatmap", "histogram", "scatter", "structure"),
  ...
)

Arguments

`x`	An object inheriting from class `flash`.
`include_scree`	This parameter has been deprecated; please use `plot_type` instead.
`include_pm`	This parameter has been deprecated; please use `plot_type` instead.
`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`, or, if `pm_groups = NULL`, a vector specifying a color for each plotted row `i` or column `j`. For effects, see parameter `plot_type`.
`plot_type`	The type of plot to return. Options include: `"scree"` A scree plot showing the proportion of variance explained per factor/loadings pair. See `flash_plot_scree`. `"bar"` A bar plot of posterior means for loadings or factors (depending on argument `pm_which`), with one bar per row or column. Colors of bars are specified by argument `pm_colors`. This type of plot is most useful when rows or columns are small in number or ordered in a logical fashion (e.g., spatially). See `flash_plot_bar`. `"heatmap"` A heatmap showing posterior means for loadings or factors, with rows or columns grouped using a 1-d embedding. Here `pm_color` specifies the diverging color gradient (low-mid-high). See `flash_plot_heatmap`. `"histogram"` Overlapping semi-transparent histograms of posterior means for loadings or factors, with one histogram per group specified by `pm_groups` (or a single histogram if `pm_groups` is `NULL`). Colors of histograms are specified by `pm_colors`. See `flash_plot_histogram`. `"scatter"` A scatter plot showing the relationship between posterior means for loadings or factors and a user-supplied covariate. If a covariate is not supplied, then data column or row means will be used. Colors of points are specified by `pm_colors`. See `flash_plot_scatter`. `"structure"` A "structure plot" (stacked bar plot) produced using function `structure_plot` in package `fastTopics`. Here `pm_colors` specifies the colors of different factor/loadings pairs (as specified by `kset`) rather than different groups (as specified by `pm_groups`). Note that factors/loadings must be nonnegative for structure plots to make sense. See `flash_plot_structure`.
`...`	Additional parameters to be passed to respective `flash_plot_xxx` functions. See `flash_plot_scree`, `flash_plot_bar`, `flash_plot_heatmap`, `flash_plot_histogram`, `flash_plot_scatter`, and `flash_plot_structure` for details.