DEcomparisonPlot: DEcomparisonPlot

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

DEcomparisonPlot

Description

A function to visualise the pairwise comparison of pvalue in different data modality.

Usage

DEcomparisonPlot(de_list, feature_list)

Arguments

de_list	A list including two lists results from 'DE genes ()'.
feature_list	A list including two lists features indicating the selected subset of features will be visualised

Value

A ggplot2 to visualise the comparison plot of DE.

Examples

library(S4Vectors)
data(sce_control_subset)
sce_control_subset <- DEgenes(sce_control_subset,
group = sce_control_subset$SNF_W_louvain,
return_all = TRUE,
exprs_pct = 0.5)

sce_control_subset <- selectDEgenes(sce_control_subset)

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_list <- c("hg19_CD4",
"hg19_CD8A",
"hg19_HLA-DRB1",
"hg19_ITGAX",
"hg19_NCAM1",
"hg19_CD27",
"hg19_CD19")

adt_list <- c("CD4", "CD8", "MHCII (HLA-DR)", "CD11c", "CD56", "CD27", "CD19")

rna_DEgenes_all <- S4Vectors::metadata(sce_control_subset)[["DE_res_RNA"]]
adt_DEgenes_all <- S4Vectors::metadata(sce_control_subset)[["DE_res_ADT"]]

feature_list <- list(RNA = rna_list, ADT = adt_list)
de_list <- list(RNA = rna_DEgenes_all, ADT = adt_DEgenes_all)

DEcomparisonPlot(de_list = de_list,
                 feature_list = feature_list)

SydneyBioX/CiteFuse documentation built on Feb. 13, 2023, 6:04 a.m.