Plot top genes per LV by Z loading

For each selected latent variable, ranks genes by their Z loading and plots the top genes as a loading-versus-rank scatter plot. The highest ranking genes are labelled with ggrepel.

Usage

CLAMPplotTopZ(
  clampRes,
  data = NULL,
  priorMat = NULL,
  top = 50,
  index = NULL,
  allLVs = FALSE,
  label.top = min(10, top),
  max.name.len = 50
)

Arguments

clampRes

A CLAMP result list containing at least Z, and optionally U for selecting LVs with pathway support.

data

Deprecated; retained for backward compatibility and ignored.

priorMat

Deprecated; retained for backward compatibility and ignored.

top

Number of top genes to plot per LV. Default 50.

index

Integer or character vector of LV columns to include. NULL keeps LVs with non-zero U entries when U is present.

allLVs

Logical; if TRUE, all LVs are eligible when index = NULL. Default FALSE.

label.top

Number of top genes to label per LV. Default min(10, top).

max.name.len

Maximum characters for displayed gene labels.

Value

A ggplot2::ggplot() object for one LV, or a patchwork object for multiple LVs.

Examples

set.seed(1)
genes <- paste0("Gene", 1:80)
lvs <- paste0("LV", 1:4)
paths <- paste0("Path", 1:10)
Z <- matrix(abs(rnorm(80 * 4)),
    nrow = 80,
    dimnames = list(genes, lvs)
)
U <- matrix(abs(rnorm(10 * 4)),
    nrow = 10,
    dimnames = list(paths, lvs)
)
clampRes <- list(Z = Z, U = U)
CLAMPplotTopZ(clampRes, top = 20, index = 1:2)