[27]:

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

Fig6 all DCs#

[28]:


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")

[29]:

DC <- readRDS("V1_Celltype_allDC_2nd_withAnnotation.rds")
DC@meta.data$cell.type.sub3 <- "LAMP3+ DC"
DC@meta.data[DC@meta.data$cell.type.sub2 == "DC – CD1C+CLEC10A+", "cell.type.sub3"] <- "CD1c+ DC"
DC@meta.data[DC@meta.data$cell.type.sub2 == "DC – CD207+CD1E+", "cell.type.sub3"] <- "Langerin+ DC"
DC@meta.data[DC@meta.data$cell.type.sub2 == "DC – CLEC9A+WDFY4+", "cell.type.sub3"] <- "CD141+ DC"
DC@meta.data[DC@meta.data$cell.type.sub2 == "pDC – TCF4+IL3RA+", "cell.type.sub3"] <- "pDC"

DC@meta.data$cell.type.sub3 <- factor(DC@meta.data$cell.type.sub3,
                                      levels = c("CD141+ DC", "CD1c+ DC", "Langerin+ DC", "LAMP3+ DC", "pDC"))

[30]:

DC@meta.data$status2 <- "Malignant"
DC@meta.data[DC@meta.data$status == "P", "status2"] <- "Non-Malignant"
DC@meta.data[DC@meta.data$status == "T", "status2"] <- "Malignant"

DC@meta.data$status2 <- factor(DC@meta.data$status2,levels = c("Malignant", "Non-Malignant"))

[31]:

Mye <- readRDS("/annoroad/data1/bioinfo/PROJECT/big_Commercial/Cooperation/B_TET/B_TET-072/supplement/yaojiaying/AN202202140002/Analysis/Data/V1_Celltype_Mye_3nd_withAnnotation.rds")

[32]:

Mye@meta.data$cell.type.sub3 <- Mye@meta.data$cell.type.sub2
Mye@meta.data[rownames(DC@meta.data), "cell.type.sub3"] <- as.character(DC$cell.type.sub3)
Mye@meta.data$status2 <- "Malignant"
Mye@meta.data[Mye@meta.data$status == "P", "status2"] <- "Non-Malignant"
Mye@meta.data[Mye@meta.data$status == "T", "status2"] <- "Malignant"

Mye@meta.data$status2 <- factor(Mye@meta.data$status2, levels = c("Malignant", "Non-Malignant"))

selectCells <- Cells(Mye)[Mye$cell.type.sub2 %in% c("DC – CLEC9A+WDFY4+", "DC – CD1C+CLEC10A+", "DC – CD207+CD1E+", "DC – “mregDC”", "pDC – TCF4+IL3RA+")]
deadCells <- selectCells[selectCells %in% Cells(DC) == FALSE]
length(deadCells)
Mye@meta.data[deadCells, "cell.type.sub3"] <- "deadCells"
final_Mye <- subset(Mye, cell.type.sub3 != "deadCells")

final_Mye@meta.data$status2 <- "Malignant"
final_Mye@meta.data[final_Mye@meta.data$status == "P", "status2"] <- "Non-Malignant"
final_Mye@meta.data[final_Mye@meta.data$status == "T", "status2"] <- "Malignant"

final_Mye@meta.data$status2 <- factor(final_Mye@meta.data$status2, levels = c("Malignant", "Non-Malignant"))

final_Mye <- subset(final_Mye, cell.type.sub3 != "pDC")
87
[33]:

final_Mye@meta.data$cell.type.sub3 <- gsub(" – ", " ", final_Mye@meta.data$cell.type.sub3)
Mye_levels2 <- c("neu IL1RN+","neu CMTM2+SELL+","neu IFN_signaling+","neu SLPI+MMP9+",
                "mac/mono IL10+HS_ signaling+","mac/mono EREG+inflammasome+","mac/mono RNASE1+LYVE1+","mac/mono CCL4+CLL3+CD14+","mac/mono CXCL10+TIMP1+",
                "mac/mono CDKN1C+TCF7L2+","mac/mono CCL4+CLL3+CD14-","mac/mono APOE+SPP1+",
                "CD141+ DC", "CD1c+ DC", "Langerin+ DC", "LAMP3+ DC")
final_Mye@meta.data$cell.type.sub3 <- factor(final_Mye@meta.data$cell.type.sub3, levels=rev(Mye_levels2))

[34]:

head(Mye@meta.data,2)
A data.frame: 2 × 18
orig.identnCount_RNAnFeature_RNAseurat_clusterscell.type.v1statuspatientMye.ctsub.ctRNA_snn_res.0.5RNA_snn_res.0.4RNA_snn_res.0.7RNA_snn_res.1cell.type.sub2cell.type.sub1cell.type.subcell.type.sub3status2
<fct><dbl><int><fct><fct><fct><fct><chr><chr><fct><fct><fct><fct><chr><chr><fct><chr><fct>
MIBC5P.ATGGTTGAGTGACACGMIBC5P22882.655455715MyePMIBC5cDCcDC - 010101215DC – CLEC9A+WDFY4+DCDC – CLEC9A+WDFY4+CD141+ DCNon-Malignant
MIBC5P.CGCAGGTGTTTGGGTTMIBC5P 5257.862161415MyePMIBC5cDCcDC - 310101215DC – CLEC9A+WDFY4+DCDC – CLEC9A+WDFY4+CD141+ DCNon-Malignant
 
[35]:

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"

[36]:

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

VlnPlot(final_Mye, features=c("CD274"), split.by="status2", group.by="treat",
            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))

Error in file(con, "rb"): 无法打开链结
Traceback:


plot without title

[ ]:



[8]:

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

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

VlnPlot(final_Mye, features=c("CD274"), split.by="status2", 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))

The default behaviour of split.by has changed.
Separate violin plots are now plotted side-by-side.
To restore the old behaviour of a single split violin,
set split.plot = TRUE.

This message will be shown once per session.
../../_images/notebooks_geneExp_THU-4_12_1.png 
[19]:

Fig6cFeatures <- c('CD274','PDCD1LG2','CD276','LGALS9',
                   'VSIR','TNFRSF14','CEACAM1','PVR',
                   'FGL1','VSIG4','SIGLEC10')

Fig6cFeatures2 <- c("CD274", "PDCD1LG2", "CD276", "LGALS9",
                    "HAVCR2", "VSIR", "BTLA", "TNFRSF14",
                    "CEACAM1", "PVR", "FGL1",
                    "VSIG4", "SIGLEC10")

options(repr.plot.width=9, repr.plot.height=6)

DotPlot(final_Mye, features=Fig6cFeatures2, group.by="cell.type.sub3", cols = c("#F5F5F5", "red")) +
    theme(axis.text.x=element_text(angle=45,hjust=1,size=12)) + xlab("") + ylab("")

ggsave("Fig6A_dotplot_all.pdf",w=9,h=7)
../../_images/notebooks_geneExp_THU-4_13_0.png 
[20]:

DotPlot(subset(final_Mye, status2=="Non-Malignant"), features=Fig6cFeatures2, group.by="cell.type.sub3", cols = c("#F5F5F5", "red")) +
    theme(axis.text.x=element_text(angle=45,hjust=1,size=12)) + xlab("") + ylab("")

ggsave("Fig6A_dotplot_Non-Malignant.pdf",w=9,h=7)
../../_images/notebooks_geneExp_THU-4_14_0.png 
[21]:

DotPlot(subset(final_Mye, status2=="Malignant"), features=Fig6cFeatures2, group.by="cell.type.sub3", cols = c("#F5F5F5", "red")) +
    theme(axis.text.x=element_text(angle=45,hjust=1,size=12)) + xlab("") + ylab("")

ggsave("Fig6A_dotplot_Malignant.pdf",w=9,h=7)
../../_images/notebooks_geneExp_THU-4_15_0.png 
[ ]:



[12]:

options(repr.plot.width=9, repr.plot.height=6)

final_Mye@meta.data$cell.type.sub3 <- factor(final_Mye@meta.data$cell.type.sub3, levels=Mye_levels2)
Idents(final_Mye) <- "cell.type.sub3"


VlnPlot(final_Mye,features="CD274", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_CD274_all.pdf",w=9,h=6)

VlnPlot(final_Mye,features="HAVCR2", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_HAVCR2_all.pdf",w=9,h=6)

VlnPlot(final_Mye,features="BTLA", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_BTLA_all.pdf",w=9,h=6)
../../_images/notebooks_geneExp_THU-4_17_0.png
../../_images/notebooks_geneExp_THU-4_17_1.png
../../_images/notebooks_geneExp_THU-4_17_2.png 
[13]:

options(repr.plot.width=9, repr.plot.height=6)

VlnPlot(subset(final_Mye, status2=="Malignant"),features="CD274", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_CD274_Malignant.pdf",w=9,h=6)

VlnPlot(subset(final_Mye, status2=="Malignant"),features="HAVCR2", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_HAVCR2_Malignant.pdf",w=9,h=6)

VlnPlot(subset(final_Mye, status2=="Malignant"),features="BTLA", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_BTLA_Malignant.pdf",w=9,h=6)
../../_images/notebooks_geneExp_THU-4_18_0.png
../../_images/notebooks_geneExp_THU-4_18_1.png
../../_images/notebooks_geneExp_THU-4_18_2.png 
[14]:

options(repr.plot.width=9, repr.plot.height=6)

VlnPlot(subset(final_Mye, status2=="Non-Malignant"),features="CD274", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_CD274_Non-Malignant.pdf",w=9,h=6)

VlnPlot(subset(final_Mye, status2=="Non-Malignant"),features="HAVCR2", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_HAVCR2_Non-Malignant.pdf",w=9,h=6)

VlnPlot(subset(final_Mye, status2=="Non-Malignant"),features="BTLA", pt.size=-1, cols=my23colors[5:34]) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

ggsave("Fig6A_Vln_BTLA_Non-Malignant.pdf",w=9,h=6)
../../_images/notebooks_geneExp_THU-4_19_0.png
../../_images/notebooks_geneExp_THU-4_19_1.png
../../_images/notebooks_geneExp_THU-4_19_2.png 
[15]:

options(repr.plot.width=9, repr.plot.height=6)

VlnPlot(final_Mye, features="CD274", split.by="status2", pt.size=-1, cols = c('#EE8084','#19BBC1')) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")


VlnPlot(final_Mye,features="HAVCR2", split.by="status2", pt.size=-1, cols = c('#EE8084','#19BBC1')) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")


VlnPlot(final_Mye,features="BTLA", split.by="status2", pt.size=-1, cols = c('#EE8084','#19BBC1')) +
    xlab('') + theme(legend.position='none') +
    theme(axis.text.x=element_text(angle=70,hjust=1,size=12)) + ylab("")

../../_images/notebooks_geneExp_THU-4_20_0.png
../../_images/notebooks_geneExp_THU-4_20_1.png
../../_images/notebooks_geneExp_THU-4_20_2.png 
[16]:

#saveRDS(final_Mye, "final_Mye.RDS")

[ ]:



[ ]:



[ ]: