Plot eigengene distributions per cell type and species

Plots the distribution of eigengenes (or other types of summarized module expression profiles) per cell type and species, and thus allows the expression patterns to be visually compared across species.

Usage

plotEigengenesViolin(
  eigengenes,
  expr_column = "eigengene",
  cell_type_column = "cell_type",
  species_colors = NULL,
  font_size = 14
)

Arguments

eigengenes

Data frame of eigengenes, required columns:

cell: Character, the cell barcode.
species: Character, the name of the species.
{{cell_type_column}}: Character, cell type annotation.
module: Character, transcriptional regulator and in case the eigengene was calculated for the positively or negatively regulated targets only, the direction of regulation (format: nameOfRegulator(+) or nameOfRegulator(-)).
{{expr_column}}: Numeric, summarized module expression profiles (typically the eigengene, the mean expression of the module, or the expression of the regulator).

expr_column

Character specifying which column of eigengenes the heatmap should be colored by. This column is expected to contain summarized module expression profiles, typically the eigengene (default: "eigengene"), the mean expression of the module, or the expression of the regulator.

cell_type_column

Character, the name of the cell type annotation column in eigengenes.

species_colors

Character vector, colors per species.

font_size

Numeric, font size (default: 14).

Value

A violin plot as a ggplot object showing the expression distributions of the modules per cell type and species.

Details

A concept adapted from WGCNA, the eigengene summarizes the expression profile of an entire module, and it is calculated as the first principal component of the module expression data (see also calculateEigengenes). Other possible ways of representing the expression profile of a module include the mean expression and the regulator expression.

The function takes a data frame containing any of these summarized module expression profiles as input (normally the output of calculateEigengenes). The column containing the chosen type of summarized expression profile can be specified by the parameter expr_column (default: "eigengene").

The values of the chosen metric are plotted as violin plots per cell type and species, faceted by module. The colors for the species can be controlled by the parameter species_colors.

References

Zhang, B., & Horvath, S. (2005). A general framework for weighted gene co-expression network analysis. Statistical Applications in Genetics and Molecular Biology, 4, 17-60. https://doi.org/10.2202/1544-6115.1128

Examples

plotEigengenesViolin(eigengenes)