make_mushroom_plot: Make a "mushroom plot" of ligand-receptor interactions

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

Make a "mushroom plot" of ligand-receptor interactions

Description

make_mushroom_plot Make a plot in which each glyph consists of two semicircles corresponding to ligand- and receptor- information. The size of the semicircle is the percentage of cells that express the protein, while the saturation corresponds to the scaled average expression value.

Usage

make_mushroom_plot(
  prioritization_table,
  top_n = 30,
  show_rankings = FALSE,
  show_all_datapoints = FALSE,
  true_color_range = TRUE,
  use_absolute_rank = FALSE,
  size = "scaled_avg_exprs",
  color = "scaled_p_val_adapted",
  ligand_fill_colors = c("#DEEBF7", "#08306B"),
  receptor_fill_colors = c("#FEE0D2", "#A50F15"),
  unranked_ligand_fill_colors = c(alpha("#FFFFFF", alpha = 0.2), alpha("#252525", alpha =
    0.2)),
  unranked_receptor_fill_colors = c(alpha("#FFFFFF", alpha = 0.2), alpha("#252525", alpha
    = 0.2)),
  ...
)

Arguments

prioritization_table	A prioritization table as generated by generate_prioritization_tables.
top_n	An integer indicating how many ligand-receptor pairs to show
show_rankings	A logical indicating whether to show the ranking of the ligand-receptor pairs (default: FALSE)
show_all_datapoints	A logical indicating whether to show all ligand-receptor pairs (default: FALSE, if true they will be grayed out)
true_color_range	A logical indicating whether to use the default color range as determined by ggplot (TRUE, default) or set the limits to a range of 0-1 (FALSE)
use_absolute_rank	A logical indicating to whether use the absolute prioritization rank to filter the top_n ligand-receptor pairs (default: FALSE)
size	A string indicating which column to use for the size of the semicircles (default: "scaled_avg_exprs"; use column name without "_ligand" or "_receptor" suffix)
color	A string indicating which column to use for the color of the semicircles (default: "scaled_p_val_adapted"; use column name without "_ligand" or "_receptor" suffix)
ligand_fill_colors	A vector of the low and high colors to use for the ligand semicircle fill gradient (default: c("#DEEBF7", "#08306B"))
receptor_fill_colors	A vector of the low and high colors to use for the receptor semicircle fill gradient (default: c("#FEE0D2", "#A50F15"))
unranked_ligand_fill_colors	A vector of the low and high colors to use for the unranked ligands when show_all_datapoints is TRUE (default: c(alpha("#FFFFFF", alpha=0.2), alpha("#252525", alpha=0.2)))
unranked_receptor_fill_colors	A vector of the low and high colors to use for the unranked receptors when show_all_datapoints is TRUE (default: c(alpha("#FFFFFF", alpha=0.2), alpha("#252525", alpha=0.2)))
...	Additional arguments passed to ggplot2::theme. As there are often issues with the scales legend, it is recommended to change legend sizes and positions using this argument, i.e., legend.key.height, legend.key.width, legend.title, and legend.text.

Details

If the values range of the column used as the "size" parameter is not between 0 and 1.001, an error will be thrown.

The sender cell types can be ordered by encoding the "sender" column as a factor. If the "sender" column is not a factor, the sender cell types will be ordered alphabetically.

By default, the top_n ligand-receptor pairs are shown despite their absolute ranking. So, if a receiver cell type has LR pairs that are only ranked from 31-40 and the top_n is set to 20, the LR pairs will be shown. If use_absolute_rank is set to TRUE, only LR pairs with absolute ranking from 1-20 will be shown.

Value

A ggplot object

Examples

## Not run: 
# Create a prioritization table
prior_table <- generate_prioritization_tables(processed_expr_table, processed_DE_table, ligand_activities, processed_condition_markers, prioritizing_weights)
make_mushroom_plot(prior_table)


# Show only top 20, and write rankings on the plot
make_mushroom_plot(prior_table, top_n = 20, show_rankings = TRUE)

# Show all datapoints, and use true color range
make_mushroom_plot(prior_table, show_all_datapoints = TRUE, true_color_range = TRUE)


# Change the size and color columns
make_mushroom_plot(prior_table, size = "pct_expressed", color = "scaled_avg_exprs")


# For a prioritization table with multiple receiver cell types
make_mushroom_plot(prior_table_combined %>% filter(receiver == celltype_oi))

## End(Not run)

saeyslab/nichenetr documentation built on Sept. 7, 2024, 10:27 a.m.