library(Seurat)
library(openxlsx)
library (Hmisc)
library(dplyr)
library(patchwork)
library(ggplot2)
library(ggalluvial)
library(svglite)
library(Seurat)
所需文件的格式
load(file = “G:/silicosis/sicosis/silicosis-1122-merge/silicosis_cluster_merge.rds”)
#通过transferanchor得到的
load(file = “G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/wildtype_mouse_lung_query.rds”)
cluster_gene_stat=read.xlsx(“G:/silicosis/sicosis/silicosis_ST/overlapped_map/Rigional and cell markers.xlsx”,
sheet = “Addition”)
head(cluster_gene_stat)
cluster_gene_stat[,1]
colnames(cluster_gene_stat)
dim(cluster_gene_stat)
cluster_marker = list()
for(i in 1:ncol(cluster_gene_stat)){ #按照p0.05值、flodchange 1标准 获得11个cluster的marker基因 列表
#i=1 #因为某列可能为空值 可能会报错
cluster_marker[[paste(“col”,i, colnames(cluster_gene_stat)[i], sep = “_”)]] <- try(capitalize(unique(cluster_gene_stat[,i])),
silent = TRUE) #加unique去重复
}
head(cluster_marker)
unlist(lapply(cluster_marker, length))
cluster_gene_stat$ig-producing.b.cell
‘’’
names(cluster_marker)
#以clara细胞为例
cluster_gene_stat$“macroph-1”
cellname=“macroph-1”
mymarkers=cluster_marker[[1]]
mymarkers
mymarkers<-capitalize(mymarkers) %>% na.omit()
mymarkers
length(mymarkers)
markers=mymarkers[11:21]
markers
getwd()
cellname
‘’’
#批量做气泡图 Dotplot 如果运行出错 就一个个改循环
getwd()
file=“G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/dotplot_for_selected_genes”
file=“G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/dotplot_for_selected_genes/wild_mouse_dotplot”
dir.create(file)
setwd(file)
length(cluster_marker)
for (j in 1:length(cluster_marker)) {#一定要记得是向量 而不是一个数 for j in(1:11) 一定记得加括号！！！！！！！！！！！！
#j=1
times=(length(cluster_marker[[j]])+10)/10
times
if (floor(times)>=2 ){
try(for (i in seq(1,100,10)) { #使用循环出图 画图 以最多的基因数目为准！！！！！！！！！！！！！！！try忽略报错！！！1
#i=1
if ((i+9)>(10*floor(times))) {next}
# print(cluster_marker[[j]][i:(i+9)])
jpeg(paste0(“col_”,j,"",paste0(unlist(strsplit(cluster_marker[[j]][i:(i+2)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query, #可以改名字换成想要画的seurat对象
features = cluster_marker[[j]][i:(i+9)])
print§
dev.off()
print(paste0(“clo_”,j))#;print(cluster_marker[[j]][i:(i+9)])
} ,silent = TRUE)
} else{ #条件一定记得加括号！ ！！！！！！！！！！！！！！！11！！！！！！！！！！！
print(paste0(“col_”,j))#; print(cluster_marker[[j]][1:(1+9)])
jpeg(paste0(“col_”,j,"",paste0(unlist(strsplit(cluster_marker[[j]][1:(1+2)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query,features = cluster_marker[[j]][1:(1+9)])
print§
dev.off()
}
}
while (dev.off()) {dev.off()} #循环关闭画板
head(cluster_marker)
names(cluster_marker)
for (j in 1:length(cluster_marker)) {#一定要记得是向量 而不是一个数 for j in(1:11) 一定记得加括号！！！！！！！！！！！！
#j=1
times=(length(cluster_marker[[j]])+10)/10
times
if (floor(times)>=2 ){
try(for (i in seq(1,100,10)) { #使用循环出图 画图 以最多的基因数目为准！！！！！！！！！！！！！！！try忽略报错！！！1
#i=1
if ((i+9)>(10*floor(times))) {next}
# print(cluster_marker[[j]][i:(i+9)])
jpeg(paste0(names(cluster_marker)[j],"",
paste0(unlist(strsplit(cluster_marker[[j]][i:(i+9)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),
height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query, #可以改名字换成想要画的seurat对象
features = cluster_marker[[j]][i:(i+9)])
print§
dev.off()
print(paste0(“clo_”,j))#;print(cluster_marker[[j]][i:(i+9)])
} ,silent = TRUE)
} else{ #条件一定记得加括号！ ！！！！！！！！！！！！！！！11！！！！！！！！！！！
print(paste0(“col_”,j))#; print(cluster_marker[[j]][1:(1+9)])
jpeg(paste0(names(cluster_marker)[j],"",
paste0(unlist(strsplit(cluster_marker[[j]][1:(1+9)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),
height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query,features = cluster_marker[[j]][1:(1+9)])
print§
dev.off()
}
}
getwd()
dir.create(“G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/dotplot_for_selected_genes/wild_mouse_dotplot-groups”)
setwd(“G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/dotplot_for_selected_genes/wild_mouse_dotplot-groups”)
#改变分组方式
for (j in 1:length(cluster_marker)) {#一定要记得是向量 而不是一个数 for j in(1:11) 一定记得加括号！！！！！！！！！！！！
#j=1
times=(length(cluster_marker[[j]])+10)/10
times
if (floor(times)>=2 ){
try(for (i in seq(1,100,10)) { #使用循环出图 画图 以最多的基因数目为准！！！！！！！！！！！！！！！try忽略报错！！！1
#i=1
if ((i+9)>(10*floor(times))) {next}
# print(cluster_marker[[j]][i:(i+9)])
jpeg(paste0(names(cluster_marker)[j],"",
paste0(unlist(strsplit(cluster_marker[[j]][i:(i+9)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),
height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query, #可以改名字换成想要画的seurat对象
features = cluster_marker[[j]][i:(i+9)],
group.by = “predicted.id”) #!!!而不是split.by
print§
dev.off()
print(paste0(“clo_”,j))#;print(cluster_marker[[j]][i:(i+9)])
} ,silent = TRUE)
} else{ #条件一定记得加括号！ ！！！！！！！！！！！！！！！11！！！！！！！！！！！
print(paste0(“col_”,j))#; print(cluster_marker[[j]][1:(1+9)])
jpeg(paste0(names(cluster_marker)[j],"",
paste0(unlist(strsplit(cluster_marker[[j]][1:(1+9)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),
height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query,
features = cluster_marker[[j]][1:(1+9)],
group.by = “predicted.id”)
print§
dev.off()
}
}
while (dev.off()) {dev.off()} #循环关闭画板
getwd()
dir.create(“G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/dotplot_for_selected_genes/wild_mouse_dotplot-groups_elegant/for_wild_”,
recursive = TRUE)
setwd(“G:/silicosis/geo/GSE164621_RNA-seq_wildtype_mouse_lung/dotplot_for_selected_genes/wild_mouse_dotplot-groups_elegant/for_wild_”)
for (j in 1:length(cluster_marker)) {#一定要记得是向量 而不是一个数 for j in(1:11) 一定记得加括号！！！！！！！！！！！！
#j=1
times=(length(cluster_marker[[j]])+10)/10
times
if (floor(times)>=2 ){
try(for (i in seq(1,100,10)) { #使用循环出图 画图 以最多的基因数目为准！！！！！！！！！！！！！！！try忽略报错！！！1
#i=1
if ((i+9)>(10*floor(times))) {next}
# print(cluster_marker[[j]][i:(i+9)])
jpeg(paste0(names(cluster_marker)[j],"",
paste0(unlist(strsplit(cluster_marker[[j]][i:(i+9)], " "))[seq(1,10,1)],seq=’’,collapse = “”) , “.jpeg”),
height = 9, width = 18, units = ‘in’, res=300)
p=DotPlot(wildtype_mouse_lung.query, #可以改名字换成想要画的seurat对象
features = cluster_marker[[j]][i:(i+9)],
group.by = “predicted.id”) #!!!而不是split.by
print§
dev.off()
print(paste0(“clo_”,j))#;print(cluster_marker[[j]][i:(i+9)])
} ,silent = TRUE)
} else{ #条件一定记得加括号！ ！！！！！！！！！！！！！！！11！！！！！！！！！！！
try(if(1==1){print(paste0("col_",j))#; print(cluster_marker[[j]][1:(1+9)])
jpeg(paste0(names(cluster_marker)[j],"_",
paste0(unlist(strsplit(cluster_marker[[j]][1:(1+9)], " "))[seq(1,10,1)],seq='_',collapse = "") , ".jpeg"),
height = 9, width = 18, units = 'in', res=300)
p=DotPlot(wildtype_mouse_lung.query,
features = cluster_marker[[j]][1:(1+9)],
group.by = "predicted.id")
print(p)
dev.off()},silent = TRUE)
}
}
结果图 10个为一组 输出所有基因的dotplot图气泡图
#方式二 把所有列都读入列表
cluster_marker = list()
for(i in 1:ncol(cluster_gene_stat)){ #循环读取excel里的不同列
#i=1
cluster_marker[[paste(“col”,i, colnames(cluster_gene_stat)[i], sep = “_”)]] <- capitalize(na.omit(unique(cluster_gene_stat[,i])))#加unique去重复
}
nchar(cluster_marker[[1]])
head(cluster_marker)
unlist(lapply(cluster_marker, length))
cluster_marker=na.omit(cluster_marker)
head(cluster_marker)
na.omit(unique(cluster_gene_stat[,i]))
cluster_marker[[1]][4]