DEbubblePlot: DEbubblePlot

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

Description

A function to generate circlepack plot to visualise the marker for each cluster

Usage

DEbubblePlot(de_list)

Arguments

de_list

A list of results from 'DE genes ()'

Value

A ggplot to visualise the DE results via bubble plot

Examples

library(S4Vectors)
data(sce_control_subset, package = "CiteFuse")
sce_control_subset <- DEgenes(sce_control_subset,
altExp_name = "none",
group = sce_control_subset$SNF_W_louvain,
return_all = TRUE,
exprs_pct = 0.5)


sce_control_subset <- selectDEgenes(sce_control_subset,
                            altExp_name = "none")

sce_control_subset <- DEgenes(sce_control_subset,
altExp_name = "ADT",
group = sce_control_subset$SNF_W_louvain,
return_all = TRUE,
exprs_pct = 0.5)


sce_control_subset <- selectDEgenes(sce_control_subset,
                             altExp_name = "ADT")

rna_DEgenes <- metadata(sce_control_subset)[["DE_res_RNA_filter"]]
adt_DEgenes <- metadata(sce_control_subset)[["DE_res_ADT_filter"]]

rna_DEgenes <- lapply(rna_DEgenes, function(x){
  x$name <- gsub("hg19_", "", x$name)
  x})
DEbubblePlot(list(RNA = rna_DEgenes, ADT = adt_DEgenes))

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