A function to visualise ligand receptor analysis
visLigandReceptor( sce, type = c("pval_heatmap", "pval_dotplot", "group_network", "group_heatmap", "lr_network"), receptor_type = NULL )
sce | A singlecellexperiment object |
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type | A character indicates the type of the plot for ligand receptor restuls visualisation, option includes "pval_heatmap", "pval_dotplot", "group_network", "group_heatmap", and "lr_network" |
receptor_type | A character indicates which receptor expression's ligand receptor results are used to generate the figures. |
A plot visualise the ligand receptor results
data(lr_pair_subset, package = "CiteFuse") data(sce_control_subset, package = "CiteFuse") sce_control_subset <- normaliseExprs(sce = sce_control_subset, altExp_name = "ADT", transform = "zi_minMax") sce_control_subset <- normaliseExprs(sce = sce_control_subset, altExp_name = "none", exprs_value = "logcounts", transform = "minMax") sce_control_subset <- ligandReceptorTest(sce = sce_control_subset, ligandReceptor_list = lr_pair_subset, cluster = sce_control_subset$SNF_W_louvain, RNA_exprs_value = "minMax", use_alt_exp = TRUE, altExp_name = "ADT", altExp_exprs_value = "zi_minMax", num_permute = 100)#> 100 ......visLigandReceptor(sce_control_subset, type = "pval_heatmap", receptor_type = "ADT")