flash_plot_heatmap: Create heatmap of factors or loadings for a flash fit
In willwerscheid/flashier: Empirical Bayes Matrix Factorization

flash_plot_heatmap

R Documentation

Create heatmap of factors or loadings for a flash fit

Description

Creates a heatmap of 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).

Usage

flash_plot_heatmap(
  fl,
  order_by_pve = FALSE,
  kset = NULL,
  pm_which = c("factors", "loadings"),
  pm_subset = NULL,
  pm_groups = NULL,
  pm_colors = NULL,
  gap = 1,
  ...
)

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 of length 1, 2, or 3 defining the diverging color gradient (low-mid-high) to be used by the heatmap. The midpoint is set at zero. If one or two colors are supplied, then the "mid" color will be set to white. If one color is supplied, then the "low" and "high" colors (used for, respectively, negative and positive posterior means) will be the same. If two are supplied, then the "low" color should be provided first, followed by the "high" color. If all three are supplied, then the "low" color should be provided first, followed by the "mid" color, followed by the "high" color provided. The default color gradient is `darkblue` for "low" (negative posterior means), white for "mid" (zero), and `darkred` for "high" (positive posterior means).
`gap`	The horizontal spacing between groups. Ignored if `pm_groups` is not provided.
`...`	Additional parameters to be passed to `structure_plot` (which is primarily used to arrange the rows `i` or columns `j`).

Details

By default, a 1-d embedding is used to arrange the rows i or columns j in a "smart" manner. This behavior can be overridden via argument loadings_order, which is passed to function structure_plot.