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

Source: R/plot_profiles.R

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

plot_profiles(
  data = NULL,
  ident = NULL,
  nb_column = NULL,
  color_cluster = NULL,
  size_text_y = 5,
  size_label = 2,
  legend_name = "Cell\ntype",
  to_lin = FALSE,
  averaged = FALSE
)

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_cluster

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.

to_lin

Transform in linear scale (i.e. 2^x).

averaged

Display the mean expression averaged across cells.

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")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_2 was already loaded. 
# Load a ClusterSet object
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_clusters_2 was already loaded. 
                            
plot_profiles(lymph_node_tiny_clusters_2, ident=Seurat::Idents(lymph_node_tiny_2))
#> |-- INFO :  Number of cells types: 13 
#> |-- INFO :  Number of cells: 442 

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_cluster = pal)
#> |-- INFO :  Number of cells types: 13 
#> |-- INFO :  Number of cells: 442 

plot_profiles(lymph_node_tiny_clusters_2[2:4,], ident=Seurat::Idents(lymph_node_tiny_2), color_cluster = pal)
#> |-- INFO :  Number of cells types: 13 
#> |-- INFO :  Number of cells: 442