Factor Correlation Plot

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.

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

name of dimensionality reduction containing NMF loadings, Seurat only.

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

if (FALSE) {
Factor_Cor_Plot(object = obj)
}