make_ligand_activity_target_exprs_plot: make_ligand_activity_target_exprs_plot

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

make_ligand_activity_target_exprs_plot

Description

make_ligand_activity_target_exprs_plot Plot the ligand expression in senders plus their activity and target genes in receivers

Usage

make_ligand_activity_target_exprs_plot(receiver_oi, prioritized_tbl_oi, prioritization_tbl_ligand_receptor, prioritization_tbl_ligand_target,
exprs_tbl_ligand, exprs_tbl_target, lfc_cutoff, ligand_target_matrix, scaled_ligand_activity_limits = "abs_max", plot_legend = TRUE, heights = NULL, widths = NULL)

Arguments

receiver_oi	Name of the receiver cell type of interest
prioritized_tbl_oi	Dataframe with the ligand-receptor interactions that should be visualized
prioritization_tbl_ligand_receptor	$prioritization_tbl_ligand_receptor slot of 'get_prioritization_tables'
prioritization_tbl_ligand_target	$prioritization_tbl_ligand_target slot of 'get_prioritization_tables'
exprs_tbl_ligand	Dataframe with the expression values for the ligands in the sender cell types
exprs_tbl_target	Dataframe with the expression values for the targets in the receiver cell types
lfc_cutoff	Cutoff used on the logFC value
ligand_target_matrix	ligand-target matrix
scaled_ligand_activity_limits	limits used in the heatmap for the scaled ligand activity, one of "abs_max" (-+ absolute maximum), "min_max" (minimum and maximum), or "IQR" (cf. boxplot, outliers are squished to the limits)
plot_legend	TRUE (default): add legend to the plot. FALSE: do not add legend.
heights	automatic determination if default NULL. If not NULL: number given by the user to indicate the requested heights, which are the height proportions of the different row panels in the plot.
widths	automatic determination if default NULL. If not NULL: number given by the user to indicate the requested widths, which are the width proportions of the different columns (side-by-side heatmaps) in the plot.

Value

List containing the combined heatmap and the legend

Examples

## Not run: 
make_ligand_activity_target_exprs_plot(receiver_oi, prioritized_tbl_oi, prioritization_tbl_ligand_receptor, prioritization_tbl_ligand_target, exprs_tbl_ligand, exprs_tbl_target, lfc_cutoff, ligand_target_matrix, scaled_ligand_activity_limits = "abs_max", plot_legend = TRUE, heights = NULL, widths = NULL)

## End(Not run)

saeyslab/nichenetr documentation built on April 27, 2024, 9:24 p.m.