plot_profiles: Plot mean expression profiles of each cluster from a...

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Plot mean expression profiles of each cluster from a ClusterSet object.

Description

This function generates a barplot showing the expression profiles of cell type-specific genes across different cell types.

Usage

plot_profiles(
  data = NULL,
  ident = NULL,
  nb_column = NULL,
  color_cell_type = NULL,
  size_text_y = 5,
  size_label = 2,
  legend_name = "Cell\ntype"
)

Arguments

data	A ClusterSet object.
ident	A named vector containing the cell type identities for each cell. Typically the result from the Idents() function on a Seurat object (see Seurat library).
nb_column	The number of columns in the facet grid of the plot. If not provided, it is automatically computed as the square root of the number of cell types.
color_cell_type	A named vector of colors (with cell type as names) used to distinguish between different cell types in the plot. If not provided, the default hue color palette is used.
size_text_y	The font size of the y-axis tick labels.
size_label	The font size of the cluster labels.
legend_name	A name for the legend.

Value

A ggplot object showing the expression profiles of cell type-specific genes.

Examples

# Load a Seurat object
load_example_dataset("7870305/files/lymph_node_tiny_2")
# Load a ClusterSet object
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
                            
plot_profiles(lymph_node_tiny_clusters_2, ident=Seurat::Idents(lymph_node_tiny_2))
lv <- levels(Seurat::Idents(lymph_node_tiny_2))
pal <- discrete_palette(n=length(lv))
names(pal) <- lv
plot_profiles(lymph_node_tiny_clusters_2, ident=Seurat::Idents(lymph_node_tiny_2), color_cell_type = pal)
plot_profiles(lymph_node_tiny_clusters_2[2:4,], ident=Seurat::Idents(lymph_node_tiny_2), color_cell_type = pal)

dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.