(视频教程): Monocle2安装包测试、分析流程及可视化修饰
2024-12-17 本文已影响0人
KS科研分享与服务
前面我们刚更新完CytoTRACE2，那么也是想着用将其与monocle2分析结合起来，一方面看看效果，一方面辅助起点确定。同时近期不止有一个小伙伴在跑monocle2分析，但是还是因为包出了问题，我们之前发布过一个终集修改版2.26.0（Monocle2终极修改版），使用起来是没有问题的，但是小伙伴确有问题，这让我下定决心要找出问题。此外，也想将整个流程做一个视频讲解，弥补之前没有视频教程的遗憾，有很多小伙伴有此需求。
首先说结论，为什么终极修改包有些人出错，有些人不出错。经过我们的测试发现，安装monocle 2.26.0修改版在R 4.2中，无论是服务器还是本地电脑的运行中，ordercell和BEAM都不会出此案错误，但是在R 4.3中，ordercell没有问题，BEAM依然报错，可见2.26.0修改版与R版本有些关系。那么如果是R4.3，总不能为了monocle降级吧，我们测试发现monocle 2.32.0 在R 4.3中Ordercell没有问题，BEAM有问题，所以对2.32.0也做了修改版，让其在R 4.3中运行无障碍。（注意了：包修改的是它本身的问题，如果是因为流程或者数据的错误，需要自行检查）
接下来走走monocle2的流程吧，这里为了方便，数据也小，我们直接包装了一个函数，实际运行我们还是建议自己按照流程，因为需要中间调整参数。如果你的参数流程已经探索没有问题了，那么可以包装函数，方便分析：
library(Seurat)
library(monocle)
library(viridis)
#========================================================================================
setwd("D:\\KS项目\\公众号文章\\视频教程---monocle2分析测试")
#load data-加载之前做了cytroTRACE2的那个obj
#可以结合辅助看看cell起点
load("D:/KS项目/公众号文章/CytroTRACE2：单细胞转录组数据推断细胞发育潜能/sce_trace.RData")
DimPlot(cytotrace2_sce, label = T, pt.size = 1)
#这个数据是大群里面直接提取了目标细胞进行分析
#========================================================================================
#monocle pieline function
#pay attention---Seuratobject version 5.0.0
ks_run_Monocle2 <- function(object, #seurat obj or expression matrix (建议数据格式转为matrix,如果数据量大转化为稀疏矩阵as(as.matrix(data), "sparseMatrix"))
layer, #used when object is a seurat obj
assay, #used when object is a seurat obj
lowerDetectionLimit = 0.1,
VARgenesM=c("dispersionTable","seurat","differentialGeneTest"),
cellAnno=NULL,
define_root=F,
root_state,
reverse=NULL
){
if(class(object)[1] == 'Seurat') {
data <- GetAssayData(object=object, layer=layer, assay=assay)#get expression matrix data
pd <- new("AnnotatedDataFrame", data = object@meta.data)
fData <- data.frame(gene_short_name = row.names(data), row.names = row.names(data))
fd <- new("AnnotatedDataFrame", data = fData)
if(all(data == floor(data))) {
expressionFamily <- negbinomial.size()
} else if(any(data < 0)){
expressionFamily <- uninormal()
} else {
expressionFamily <- tobit()
}
#Creates a new CellDateSet object.
monocle_cds <- newCellDataSet(data,
phenoData = pd,
featureData = fd,
lowerDetectionLimit=0.1,
expressionFamily=expressionFamily)
}else{
print("This fucntions only apply for a seurat obj")
}
#Estimate size factors and dispersions
#数据处理
monocle_cds <- estimateSizeFactors(monocle_cds)#size facotr标准化细胞之间的mRNA差异
monocle_cds <- estimateDispersions(monocle_cds)
#质量控制-filter cells
monocle_cds <- detectGenes(monocle_cds, min_expr = 0.1)
# print(head(fData(monocle_cds)))
# print(head(pData(monocle_cds)))
# expressed_genes <- row.names(subset(fData(mouse_monocle), num_cells_expressed >= 10))
monocle_cds <- monocle_cds[fData(monocle_cds)$num_cells_expressed >= 10, ]
#select methods for VariableFeatures
if(VARgenesM=="dispersionTable"){
disp_table <- dispersionTable(monocle_cds)
ordering_genes <- subset(disp_table,
mean_expression >= 0.1 &
dispersion_empirical >= 1.5* dispersion_fit)$gene_id
}
if(VARgenesM=="seurat"){
ordering_genes <- VariableFeatures(FindVariableFeatures(object, assay = "RNA"), assay = "RNA")
}
if(VARgenesM=="differentialGeneTest"){
diff_test_res <- differentialGeneTest(monocle_cds,fullModelFormulaStr = paste0("~",cellAnno))##~后面是表示对谁做差异分析的变量
diff_test_res_sig <- diff_test_res[order(diff_test_res$qval,decreasing=F),]
ordering_sce <- diff_test_res_sig[diff_test_res_sig$qval< 0.01,]
if(nrow(ordering_sce)>3000){
ordering_genes <- ordering_sce$gene_short_name[1:3000]
}else{
ordering_genes <- rdering_sce$gene_short_name
}
}
#Marks genes for clustering
monocle_cds <- setOrderingFilter(monocle_cds, ordering_genes)
plot_ordering_genes(monocle_cds)
#cluster
monocle_cds <- reduceDimension(monocle_cds, max_components = 2,reduction_method = 'DDRTree')
#order cells
monocle_cds <- orderCells(monocle_cds, reverse=reverse)
if(define_root){
monocle_cds <- monocle_cds <- orderCells(monocle_cds,root_state = root_state)
}
return(monocle_cds)
}
分析数据以及一些基本可视化修饰：
#run monocle2
sce_CDS <- ks_run_Monocle2(object = cytotrace2_sce,
layer = 'counts',
assay = "RNA",
VARgenesM="dispersionTable",
cellAnno = "cluster")
#可视化拟时
plot_cell_trajectory(sce_CDS,show_branch_points = F,color_by = "Pseudotime",cell_size = 3)+
scale_color_gradientn(colours = colorRampPalette(c('blue','green','yellow','red'))(100))
#按照celltype着色
plot_cell_trajectory(sce_CDS,show_branch_points = F,color_by = "cluster",cell_size = 3)+
theme_dr(arrow = grid::arrow(length = unit(0, "inches")))+
theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank())+
scale_color_manual(values = c("#E69253", "#EDB931", "#E4502E", "#4378A0"))+
geom_curve(aes(x=9,y=2,yend=0,xend=5),
arrow=arrow(length=unit(0.03,"npc")),
size=1,curvature=0,
color="black")+
annotate("text", x=6.5, y=1.5, label = "bold(YSMP)", parse = TRUE, angle=45, size=4)+
geom_curve(aes(x=-4,y=-1,yend=3,xend=-6),
arrow=arrow(length=unit(0.03,"npc")),
size=1,curvature=0,
color="black")+
annotate("text", x=-4, y=1, label = "bold(Monocyte~Fate)", parse = TRUE, angle=-75, size=4)+
geom_curve(aes(x=-5,y=-3,yend=-5,xend=-6),
arrow=arrow(length=unit(0.03,"npc")),
size=1,curvature=0,
color="black")+
annotate("text", x=-6.5, y=-4, label = "bold(Neu~Fate)", parse = TRUE, angle=75, size=4)
#结合可视化cytroTRACE2结果
plot_cell_trajectory(sce_CDS,show_branch_points = F,color_by = "CytoTRACE2_Relative",cell_size = 3)+
scale_colour_gradientn(colours = (c( "#000004FF", "#3B0F70FF", "#8C2981FF", "#DE4968FF", "#FE9F6DFF", "#FCFDBFFF")),
na.value = "transparent",
limits=c(0,1),
breaks = c(0,1),
labels=c("(More diff.)", "(Less diff.)"),
name = "Relative\norder \n" ,
guide = guide_colorbar(frame.colour = "black", ticks.colour = "black"))+
theme_dr(arrow = grid::arrow(length = unit(0, "inches")))+#坐标轴主题修改
theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
#=======================================================================================
#拟时差异基因
expressed_genes=row.names(subset(fData(sce_CDS),use_for_ordering=="TRUE"))
peu_gene <- differentialGeneTest(sce_CDS[expressed_genes,],fullModelFormulaStr = "~sm.ns(Pseudotime)",cores = 1)
# write.csv(peu_gene,file='peu_gene.csv')#保存好文件，这个分析过程挺费时间
peu_gene <- peu_gene[which(peu_gene$qval<0.01 & peu_gene$num_cells_expressed>100),]#筛选显著是的
# peu_gene %>% arrange(qval) -> peu_gene#按照qval排个序
# peu_gene <- peu_gene[1:100,] #这里我们取前100个基因演示
#改造热图函数，展示需要的基因
source('./new_heatmap.R')
library(pheatmap)
library(grid)
p1 <-plot_pseudotime_heatmap(sce_CDS[peu_gene$gene_short_name,],
num_clusters = 4,
cores = 2,
show_rownames = T,return_heatmap =T,
hmcols = viridis(256),
use_gene_short_name = T,
clustercolor = c("#d2981a", "#a53e1f", "#457277", "#8f657d"))
p1
#只展示感兴趣的基因
genes <- c("C1QB","C1QC","C1QA","MRC1","LGMN","MS4A7","MAF","FOLR2",
"HLA-DPA1","CLEC10A","IL10RA","CD163","KCTD12","CLEC7A","MS4A6A","CD14",
"ITM2A","CYTL1","MDK","SELP","CD24",
"S100A8","S100A9","S100A12")
source('./add.flag.R')
add.flag(p1, kept.labels = genes, repel.degree = 0.2)
library(RColorBrewer)
plot_cell_trajectory(sce_CDS,show_branch_points = T,color_by = "State",cell_size = 3)
#BEAM
#查看在分叉处的差异基因
BEAM_res <- BEAM(sce_CDS, branch_point = 3, cores=2)
BEAM_res <- BEAM_res[order(BEAM_res$qval),]
BEAM_res <- BEAM_res[,c("gene_short_name", "pval", "qval")]
# write.csv(BEAM_res,file = "BEAM_res.csv")
branch_p <- plot_genes_branched_heatmap(sce_CDS[row.names(subset(BEAM_res, qval < 1e-8)),],
branch_point = 3,
num_clusters = 4,
cores = 2,
hmcols = colorRampPalette(c("steelblue", "white","darkorange2", "orangered4"))(100),
use_gene_short_name = T,
show_rownames = T,
return_heatmap = T)
总之，整个流程是比较简单的，最重要的自己对于结果的把握和解释，以及一些新的发现。希望我们的流程对您有所帮助！
