Factor_Cor_Plot: Factor Correlation Plot

In samuel-marsh/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. Any negative correlations are set to NA and NA values set to bottom color of color gradient.

Usage

Factor_Cor_Plot(
  object,
  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.
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.
cluster_rect_num	number of rectangles to add to the plot, default NULL.
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)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.