Liana dotplot interactions by source and target cells
Usage
liana_dotplot(
liana_res,
source_groups = NULL,
target_groups = NULL,
ntop = NULL,
specificity = "natmi.edge_specificity",
magnitude = "sca.LRscore",
y.label = "Interactions (Ligand -> Receptor)",
size.label = "Interaction\nSpecificity",
colour.label = "Expression\nMagnitude",
show_complex = TRUE,
size_range = c(2, 10),
invert_specificity = FALSE,
invert_magnitude = FALSE,
invert_function = function(x) -log10(x + 1e-10)
)Arguments
- liana_res
aggregated `liana_wrap` results from multiple methods, or alternatively results from running `liana_wrap` with a single method. Should be filtered by some condition (e.g. preferential consesus ranking, specific interactions, etc).
- source_groups
names of the source (sender) cell types (NULL = no filter)
- target_groups
names of the target cell types (NULL = no filter)
- ntop
number of interactions to return. Note that this assumes that the tibble is sorted in descending order of interaction importance!
- specificity
column to represent the dot-size of the interaction (by default `natmi.edge_specificity`)
- magnitude
column to represent interactions expression magnitude (by default `sca.LRscore`)
- y.label
y label name
- size.label
size (~specificty) label name
- colour.label
colour (~magnitude) label name
- show_complex
logical whether to show complexes (default - TRUE) or only the subunit with minimum expression.
Details
Here, we refer to `specificity` as how specific this interaction is to a cell type pair regards to the rest of the cell type pairs ( e.g. CellPhoneDB's p-values, NATMI's specificity edges, Connectome's scaled weights, etc)
`magnitude` on the other hand is a direct measure of the expression alone, by default we use SingleCellSignalR's dataset indepent LRscore (bound between 0 and 1). Yet, one could also use CellChat's probabilities or CellPhoneDB's means, etc.