liana_dotplot | R Documentation |
Liana dotplot interactions by source and target cells
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)
)
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. |
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.
a ggplot2 object
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