Factor_Cor_Plot: Factor Correlation Plot

In scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Factor Correlation Plot

Description

Plot positive correlations between gene loadings across W factor matrix in LIGER or feature loadings in reduction slot of Seurat object.

Usage

Factor_Cor_Plot(
  object,
  reduction = NULL,
  colors_use = NULL,
  label = FALSE,
  label_threshold = 0.5,
  label_size = 5,
  plot_title = NULL,
  plot_type = "full",
  positive_only = FALSE,
  x_lab_rotate = TRUE,
  cluster = TRUE,
  cluster_rect = FALSE,
  cluster_rect_num = NULL,
  cluster_rect_col = NULL
)

Arguments

object	LIGER or Seurat object.
reduction	Seurat ONLY; name of dimensionality reduction containing NMF loadings.
colors_use	Color palette to use for correlation values. Default is RColorBrewer::RdBu if positive_only = FALSE. If positive_only = TRUE the default is viridis. Users can also supply vector of 3 colors (low, mid, high).
label	logical, whether to add correlation values to plot result.
label_threshold	threshold for adding correlation values if label = TRUE. Default is 0.5.
label_size	size of correlation labels
plot_title	Plot title.
plot_type	Controls plotting full matrix, or just the upper or lower triangles. Accepted values are: "full" (default), "upper", or "lower".
positive_only	logical, whether to limit the plotted values to only positive correlations (negative values set to 0); default is FALSE.
x_lab_rotate	logical, whether to rotate the axes labels on the x-axis. Default is TRUE.
cluster	logical, whether to cluster the plot using hclust (default TRUE). If FALSE factors are listed in numerical order.
cluster_rect	logical, whether to add rectangles around the clustered areas on plot, default is FALSE. Uses cutree to create groups.
cluster_rect_num	number of rectangles to add to the plot, default NULL. Value is provided to k in cutree.
cluster_rect_col	color to use for rectangles, default MULL (will set color automatically).

Value

A ggplot object

Examples

## Not run: 
Factor_Cor_Plot(object = obj)

## End(Not run)

scCustomize documentation built on Dec. 11, 2025, 5:08 p.m.