visLigandReceptor: visLigandReceptor

In CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

Description

A function to visualise ligand receptor analysis

Usage

visLigandReceptor(
  sce,
  type = c("pval_heatmap", "pval_dotplot", "group_network", "group_heatmap",
    "lr_network"),
  receptor_type = NULL
)

Arguments

sce	A singlecellexperiment object
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.

Value

A plot visualise the ligand receptor results

Examples

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)
visLigandReceptor(sce_control_subset,
type = "pval_heatmap",
receptor_type = "ADT")

CiteFuse documentation built on April 14, 2021, 6 p.m.