How-to: test for cell type replicability using MetaNeighbor
Install MetaNeighbor
In R:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MetaNeighbor")
library(MetaNeighbor)
Load data
load("/data/XCGD/SCGC-GILL-JG-03_2/mono_seo.Rdata")
seo1 = seo
load("/data/XCGD/SCGC-GILL-JG-04_2/mono_seo.Rdata")
seo2 = seo
Merge data sets
colData1 = seo1@colData
colData2 = seo2@colData
colData = rbind(colData1, colData2)
data1 = seo1@assays[[1]]
data2 = seo2@assays[[1]]
m = match( rownames(data1), rownames(data2))
f.d1 = !is.na(m)
f.d2 = m[f.d1]
data1 = data1[f.d1,]
data2 = data2[f.d2,]
cd1 = paste0(colnames(data1), "_1" )
cd2 = paste0(colnames(data2), "_2" )
rownames(colData) = c(cd1,cd2)
colnames(colData)[5] = "cell_type"
study_id = c(rep(1, length(cd1)), rep(2, length(cd2)) )
names(study_id) = rownames(colData)
colData = cbind(colData, study_id)
sample_id = rownames(colData)
names(sample_id) = rownames(colData)
colData = cbind(colData, sample_id)
data = cbind(data1, data2)
colnames(data) = names(sample_id)
data = as.matrix(data)
seo = SummarizedExperiment(assays=list(counts=data), colData=colData)
Run analysis
var_genes = variableGenes(dat = seo, exp_labels = seo$study_id)
celltype_NV = MetaNeighborUS(var_genes = var_genes,
dat = seo,
study_id = seo$study_id,
cell_type = seo$cell_type)
top_hits = topHits(cell_NV = celltype_NV,
dat = seo,
study_id = seo$study_id,
cell_type = seo$cell_type,
threshold = 0.9)
cols = rev(colorRampPalette(RColorBrewer::brewer.pal(11,"RdYlBu"))(100))
breaks = seq(0, 1, length=101)
gplots::heatmap.2(celltype_NV,
margins=c(8,8),
keysize=1,
key.xlab="AUROC",
key.title="NULL",
trace = "none",
density.info = "none",
col = cols,
breaks = breaks,
offsetRow=0.1,
offsetCol=0.1,
cexRow = 2,
cexCol = 2,
ColSideCol = col.samp[samples[,1]],
RowSideCol = col.samp2[samples2[,4]]
)
