do_LigandReceptorPlot() | Cell-cell communication

This function visualizes ligand-receptor interactions between cell types using output from liana. Shows interaction magnitude and specificity as a dot plot.

Plots will be released at a later time, when Liana’s incompatibilities with Seurat v5 are solved: https://github.com/saezlab/liana/issues/200

Basic usage

First run liana:

liana_output <- liana::liana_wrap(sample) %>% 
                liana::liana_aggregate()

p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output)
p

Adjust number of interactions

p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   top_interactions = 50)
p

Sorting options

# Sort by specificity
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   sort.by = "A")

# Sort by magnitude
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   sort.by = "B")

# Sort by specificity then magnitude
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   sort.by = "C")

# Sort by magnitude then specificity
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   sort.by = "D")

# Equal weight (default)
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   sort.by = "E")

Facet by ligand or receptor

# Facet by ligand
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   split.by = "ligand.complex")

# Facet by receptor
p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   split.by = "receptor.complex")

Generate chord diagrams

p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output,
                                   compute_ChordDiagrams = TRUE)
p$DotPlot
p$ChordDiagram

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling, grid), see Shared features.

Core parameters

Parameter Description Default
liana_output Aggregated liana output —
top_interactions Number of interactions 25
top_interactions_by_group Apply per source group FALSE

Filtering

Parameter Description Default
keep_source Source cell types to keep NULL
keep_target Target cell types to keep NULL

Sorting

Parameter Description Default
sort.by Sort method (A-E) "E"
magnitude Magnitude column "sca.LRscore"
specificity Specificity column "aggregate_rank"
invert_specificity -log10 transform TRUE
invert_magnitude -log10 transform FALSE

Appearance

Parameter Description Default
dot_border Add dot borders TRUE
dot.size Dot size 1
compute_ChordDiagrams Generate chord plots FALSE

See also