suppressPackageStartupMessages({
    library(Seurat)
    library(dplyr)
    library(tidyverse)
    library(viridis)
    library(ggalluvial)
    library("ggsci")
    library("ggplot2")
    library("gridExtra")
})

DC gene expression

my23colors <- c('#53868B','#00F5FF','#C1FFC1','#0000FF','#7B68EE',
                  '#CDCD00','#FFF68F','#CD9B1D','#8B658B','#FF6A6A','#8B3A3A',
                  '#1E90FF','#FF69B4','#8DB6CD','#CAE1FF','#EECFA1','#8B7B8B',
                  '#4F4F4F','#FF4500','#BC8F8F','#FFA500','#228B22','#8B4513')

setwd("/annoroad/data1/bioinfo/PROJECT/big_Commercial/Cooperation/B_TET/B_TET-003/std/result/fanxuning/commander_test/THU")

final_Mye <- readRDS("final_Mye.RDS")

final_Mye@meta.data$treat <- "NoTreat"
final_Mye@meta.data[final_Mye@meta.data$patient == "MIBC5", "treat"] <- "Treat"
final_Mye@meta.data[final_Mye@meta.data$patient == "MIBC6", "treat"] <- "Treat"
final_Mye@meta.data[final_Mye@meta.data$patient == "MIBC8", "treat"] <- "Treat"
final_Mye@meta.data[final_Mye@meta.data$patient == "MIBC13", "treat"] <- "Treat"

options(repr.plot.width=10, repr.plot.height=5)

Idents(final_Mye) <- "cell.type.sub3"

VlnPlot(final_Mye, features=c("CD274"), split.by="treat", group.by="cell.type.sub3",
            cols = c('#EE8084','#19BBC1'),
            pt.size = 0) +
        theme(axis.ticks.x=element_blank()) +
        theme(axis.text.y=element_text(angle=0,hjust=1,size=12))

options(repr.plot.width=15, repr.plot.height=5)

VlnPlot(final_Mye, features=c("CD274","LAG3","TIGIT","CTLA-4",""), split.by="treat", group.by="cell.type.sub3",
            cols = c('#EE8084','#19BBC1'),
            pt.size = 0) +
        theme(axis.ticks.x=element_blank()) +
        theme(axis.text.y=element_text(angle=0,hjust=1,size=12))

Warning message in FetchData(object = object, vars = features, slot = slot):
“The following requested variables were not found: CTLA-4, ”