In CostaLab/scMarkerDetect: Detect marker panel from scRNA-seq profile

knitr::opts_chunk$set(echo = TRUE)

load data

You can also download the R object in "https://zenodo.org/record/5854754" manually.

suppressMessages(library(Seurat))
suppressMessages(library(sc2marker))
savedir <- "save"
dir.create(file.path(savedir))
download.file(url = "https://zenodo.org/record/5854754/files/human-PBMC%26lung.rds?download=1",
              destfile = file.path(savedir, "human_PBMC_lung.rds"), method = "curl")
human_PBMC_lung <- readRDS(file.path(savedir, "human_PBMC_lung.rds"))

# Rename Ident
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `0` = "CD4 T")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `3` = "CD4 T")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `14` = "T.Treg")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `2` = "CD8 T")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `7` = "CD8 T")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `10` = "CD8 T")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `16` = "T.Prolif")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `9` = "NK")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `6` = "B")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `13` = "B")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `8` = "B")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `20` = "B")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `11` = "Mono")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `15` = "mDC")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `17` = "pDC")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `12` = "Macro")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `1` = "Mono")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `4` = "Mono")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `5` = "Mono")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `19` = "mDC")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `18` = "Fibro")
human_PBMC_lung <- RenameIdents(object = human_PBMC_lung, `21` = "Epithelia")
human_PBMC_lung@meta.data$anno <- human_PBMC_lung@active.ident
UMAPPlot(human_PBMC_lung, label= T)

Markers for mDC cell

mDC.markers <- Detect_single_marker(human_PBMC_lung, id = "mDC", category = "Flow", org = "human", assay = "RNA.kallisto")
get_antibody(mDC.markers, org = "human")

# Ridge plot of top 9 markers of mDC cells
plot_ridge(human_PBMC_lung, id = "mDC", genes = mDC.markers[1:9,]$gene, ncol = 3, assay = "RNA.kallisto", aggr.other = F)

Markers for pDC cell

pDC.markers <- Detect_single_marker(human_PBMC_lung, id = "pDC", category = "Flow", org = "human", assay = "RNA.kallisto")
get_antibody(pDC.markers, org = "human")

# Ridge plot of top 9 markers of pDC cells
plot_ridge(human_PBMC_lung, id = "pDC", genes = pDC.markers[1:9,]$gene, ncol = 3, assay = "RNA.kallisto", aggr.other = F)

Markers for B cell

b.markers <- Detect_single_marker(human_PBMC_lung, id = "B", category = "Flow", org = "human", assay = "RNA.kallisto")
get_antibody(b.markers, org = "human")

# Ridge plot of top 9 markers of B cells
plot_ridge(human_PBMC_lung, id = "B", genes = b.markers[1:9,]$gene, ncol = 3, assay = "RNA.kallisto", aggr.other = F)

Markers for CD8 T cell

t.markers <- Detect_single_marker(human_PBMC_lung, id = "CD8 T", category = "Flow", org = "human", assay = "RNA.kallisto")
get_antibody(t.markers, org = "human")

# Ridge plot of top 9 markers of CD8 T cells
plot_ridge(human_PBMC_lung, id = "CD8 T", genes = t.markers[1:9,]$gene, ncol = 3, assay = "RNA.kallisto", aggr.other = F)

Markers for Macro

Macro.markers <- Detect_single_marker(human_PBMC_lung, id = "Macro", category = "Flow", org = "human", assay = "RNA.kallisto")
get_antibody(Macro.markers, org = "human")

# Ridge plot of top 9 markers of Macro cells
plot_ridge(human_PBMC_lung, id = "Macro", genes = Macro.markers[1:9,]$gene, ncol = 3, assay = "RNA.kallisto", aggr.other = F)

Markers for Epithelia

Epithelia.markers <- Detect_single_marker(human_PBMC_lung, id = "Epithelia", category = "Flow", org = "human", assay = "RNA.kallisto")
get_antibody(Epithelia.markers, org = "human")

# Ridge plot of top 9 markers of Epithelia cells
plot_ridge(human_PBMC_lung, id = "Epithelia", genes = Epithelia.markers[1:9,]$gene, ncol = 3, assay = "RNA.kallisto", aggr.other = F)