flash_plot_bar: Create bar plots of factors or loadings for a flash fit

In willwerscheid/flashier: Empirical Bayes Matrix Factorization

Create bar plots of factors or loadings for a flash fit

Description

Creates a bar plot or sequence of bar plots, one for each value of k in kset, with bars corresponding to individual posterior means for factors f_{jk} or loadings \ell_{ik}. 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). This type of plot is most useful when rows i = 1, \ldots, n or columns j = 1, \ldots, p are small in number or ordered in a logical fashion (e.g., spatially).

Usage

flash_plot_bar(
  fl,
  order_by_pve = FALSE,
  kset = NULL,
  pm_which = c("factors", "loadings"),
  pm_subset = NULL,
  pm_groups = NULL,
  pm_colors = NULL,
  labels = FALSE,
  ...
)

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, or, if pm_groups = NULL, a vector specifying a color for each plotted row i or column j. Defines the color (fill) of the bars.
labels	Whether to label the bars along the x-axis. The appearance of the labels (size, angle, etc.) can be adjusted using ggplot2's theme system; see below for an example.
...	Additional arguments to be passed to facet_wrap (e.g., nrow or ncol).

Details

When there is more than one value of k in kset, a sequence of panels is created using the facet_wrap function from the ggplot2 package. In each panel, the order of bars is determined by the order of the corresponding rows or columns in the data matrix; they can be re-arranged using the pm_subset argument.

Value

A ggplot object.

Examples

data(gtex)
fl <- flash(gtex, greedy_Kmax = 4L, backfit = FALSE)
flash_plot_bar(fl, pm_colors = gtex_colors)

# Tweaks are often required to get x-axis labels to look good:
library(ggplot2)
flash_plot_bar(fl, pm_colors = gtex_colors, labels = TRUE, ncol = 1) +
  theme(axis.text.x = element_text(size = 8, angle = 60))

willwerscheid/flashier documentation built on Jan. 30, 2025, 11:27 p.m.