flash_plot_scatter: Create scatter plots of factors or loadings for a flash fit

In willwerscheid/flashier: Empirical Bayes Matrix Factorization

Create scatter plots of factors or loadings for a flash fit

Description

Creates a scatter plot or sequence of scatter plots, with position along the x-axis defined by posterior means for factors f_{jk} or loadings \ell_{ik} and position along the y-axis defined by a user-supplied covariate. If a covariate is not supplied, then plots will use data column or row means, \frac{1}{n} \sum_{i = 1}^n y_{ij} or \frac{1}{p} \sum_{j = 1}^p y_{ij}. 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).

Usage

flash_plot_scatter(
  fl,
  order_by_pve = FALSE,
  kset = NULL,
  pm_which = c("factors", "loadings"),
  pm_subset = NULL,
  pm_groups = NULL,
  pm_colors = NULL,
  covariate = NULL,
  shape = 1,
  labels = FALSE,
  n_labels = 0,
  label_size = 3,
  max_overlaps = Inf,
  ...
)

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 colors of the points.
covariate	A numeric vector with one value for each plotted row i or column j. These values are mapped onto the plots' y-axis.
shape	The symbol used for the plots' points. See aes_linetype_size_shape.
labels	Whether to label the points with the largest (absolute) posterior means. If labels = TRUE, then n_labels points will be labelled using geom_text_repel.
n_labels	A (nonnegative) integer. The number of points to label. If n_labels is set to a positive integer but labels = FALSE, then the n_labels points with the largest (absolute) posterior means will be highlighted in blue but not labelled. This can be useful for tweaking labels using the full range of options provided by geom_text_repel. For an example, see below.
label_size	The size of the label text (in millimeters).
max_overlaps	A (nonnegative) integer. For each text label, the number of overlaps with other text labels or other data points are counted, and the text label is excluded if it has too many overlaps.
...	Additional arguments to be passed to facet_wrap (e.g., nrow or ncol).

Value

A ggplot object.

Examples

data(gtex)
fl <- flash(gtex, greedy_Kmax = 4L, backfit = FALSE)
flash_plot_scatter(fl)

# Label axes and points:
library(ggplot2)
flash_plot_scatter(fl, labels = TRUE, n_labels = 3) +
  labs(y = "mean z-score across all SNPs")

# For the full range of labelling options provided by the ggrepel package, set
#   labels = FALSE (the default setting) and add geom_text_repel() manually:
library(ggrepel)
flash_plot_scatter(fl, labels = FALSE, n_labels = 3) +
  geom_text_repel(size = 2.5, min.segment.length = 0)

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