Last updated: 2021-02-09

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Knit directory: Human_Development_snRNAseq/

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Rmd ffb8763 bphipson 2021-02-08 Added all analysis files
html ffb8763 bphipson 2021-02-08 Added all analysis files

Load libraries and functions

library(edgeR)
library(RColorBrewer)
library(org.Hs.eg.db)
library(limma)
library(Seurat)
library(monocle)
library(cowplot)
library(DelayedArray)
library(scran)
library(NMF)
library(workflowr)
library(ggplot2)
library(clustree)
library(dplyr)
targets <- read.delim("./data/targets.txt",header=TRUE, stringsAsFactors = FALSE)
targets$FileName2 <- paste(targets$FileName,"/",sep="")
targets$Group_ID2 <- gsub("LV_","",targets$Group_ID)
group <- c("Fetal_1","Fetal_2","Fetal_3",
           "Young_1","Young_2","Young_3",
           "Adult_1","Adult_2","Adult_3", 
           "Diseased_1","Diseased_2",
           "Diseased_3","Diseased_4")
m <- match(group, targets$Group_ID2)
targets <- targets[m,]
fetal.integrated <- readRDS(file="./output/RDataObjects/fetal-int.Rds")
load(file="./output/RDataObjects/fetalObjs.Rdata")

young.integrated <- readRDS(file="./output/RDataObjects/young-int.Rds")
load(file="./output/RDataObjects/youngObjs.Rdata")

adult.integrated <- readRDS(file="./output/RDataObjects/adult-int.Rds")
load(file="./output/RDataObjects/adultObjs.Rdata")

Set default clustering resolution

# Default 0.3
Idents(fetal.integrated) <- fetal.integrated$integrated_snn_res.0.3
DimPlot(fetal.integrated, reduction = "tsne",label=TRUE,label.size = 6)+NoLegend()

# Default 0.3
DimPlot(young.integrated, reduction = "tsne",label=TRUE,label.size = 6)+NoLegend()

# Default 0.6
DimPlot(adult.integrated, reduction = "tsne",label=TRUE,label.size = 6)+NoLegend()

Merge all data together

heart <- merge(fetal.integrated, y = c(young.integrated, adult.integrated), project = "heart")
DefaultAssay(object = heart) <- "RNA"

Get smooth muscle cells only

smc <- subset(heart,subset = Broad_celltype == "Smooth muscle cells")
dim(smc)

Check for poor quality cells

Check for cells with very low number of uniquely detected genes.

par(mfrow=c(1,2))
plot(density(smc$nFeature_RNA),main="Number of genes detected")
abline(v=500,col=2)
plot(density(smc$nCount_RNA),main="Library size")
abline(v=2500,col=2)

#smc <- subset(smc, subset = nFeature_RNA > 500 & nCount_RNA > 2500)
dim(smc)
[1] 17926   430
table(smc$biorep)

 a1  a2  a3  f1  f2  f3  y1  y2  y3 
 22  49  13  54  20 136  59  28  49 

Run new integration with SCtransform normalisation

There are very few cells for each biological replicate, so I will normalise and integrate the data by group rather than biological replicate.

smc.list <- SplitObject(smc, split.by = "orig.ident")
for (i in 1:length(smc.list)) {
    smc.list[[i]] <- SCTransform(smc.list[[i]], verbose = FALSE)
}
kf <- min(sapply(smc.list, ncol))
smc.anchors <- FindIntegrationAnchors(object.list = smc.list, dims=1:30,anchor.features = 3000,k.filter=kf)
smc.integrated <- IntegrateData(anchorset = smc.anchors,dims=1:30)

Perform clustering

DefaultAssay(object = smc.integrated) <- "integrated"

Perform scaling and PCA

smc.integrated <- ScaleData(smc.integrated, verbose = FALSE)
smc.integrated <- RunPCA(smc.integrated, npcs = 50, verbose = FALSE)
ElbowPlot(smc.integrated,ndims=50)
VizDimLoadings(smc.integrated, dims = 1:4, reduction = "pca")

DimPlot(smc.integrated, reduction = "pca",group.by="orig.ident")

DimPlot(smc.integrated, reduction = "pca",group.by="biorep")

DimPlot(smc.integrated, reduction = "pca",group.by="sex")

DimPlot(smc.integrated, reduction = "pca",group.by="batch")

DimHeatmap(smc.integrated, dims = 1:15, cells = 500, balanced = TRUE)

#DimHeatmap(smc.integrated, dims = 16:30, cells = 500, balanced = TRUE)
#DimHeatmap(smc.integrated, dims = 31:45, cells = 500, balanced = TRUE)

Perform nearest neighbours clustering

smc.integrated <- FindNeighbors(smc.integrated, dims = 1:10)
smc.integrated <- FindClusters(smc.integrated, resolution = 0.1)
table(Idents(smc.integrated))

  0   1   2 
232 174  24 
par(mfrow=c(1,1))
par(mar=c(5,4,2,2))
barplot(table(Idents(smc.integrated)),ylab="Number of cells",xlab="Clusters")
title("Number of cells in each cluster")

Visualisation with TSNE

set.seed(10)
smc.integrated <- RunTSNE(smc.integrated, reduction = "pca", dims = 1:10)
DimPlot(smc.integrated, reduction = "tsne",label=TRUE,label.size = 6,pt.size = 0.5)+NoLegend()

pdf(file="./output/Figures/tsne-smcALL-res01.pdf",width=10,height=8,onefile = FALSE)
DimPlot(smc.integrated, reduction = "tsne",label=TRUE,label.size = 6,pt.size = 0.5)+NoLegend()
dev.off()
DimPlot(smc.integrated, reduction = "tsne", group.by = "orig.ident")

DimPlot(smc.integrated, reduction = "tsne", split.by = "orig.ident")

DimPlot(smc.integrated, reduction = "tsne", group.by = "biorep")

DimPlot(smc.integrated, reduction = "tsne", group.by = "sex")

DimPlot(smc.integrated, reduction = "tsne", split.by = "sex")

DimPlot(smc.integrated, reduction = "tsne", group.by = "batch")

par(mfrow=c(1,1))
par(mar=c(4,4,2,2))
tab <- table(Idents(smc.integrated),smc.integrated$biorep)
barplot(t(tab/rowSums(tab)),beside=TRUE,col=ggplotColors(9),legend=TRUE)

par(mfrow=c(1,1))
par(mar=c(4,4,2,2))
tab <- table(Idents(smc.integrated),smc.integrated$orig.ident)
barplot(t(tab/rowSums(tab)),beside=TRUE,col=ggplotColors(3))
legend("topleft",legend=colnames(tab),fill=ggplotColors(3))

Visualisation with clustree

clusres <- c(0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1,1.1,1.2)
for(i in 1:length(clusres)){
  smc.integrated <- FindClusters(smc.integrated, 
                                   resolution = clusres[i])
}
pct.male <- function(x) {mean(x=="m")}
pct.female <- function(x) {mean(x=="f")}
pct.fetal <- function(x) {mean(x=="fetal")}
pct.young <- function(x) {mean(x=="young")}
pct.adult <- function(x) {mean(x=="adult")}
clustree(smc.integrated, prefix = "integrated_snn_res.")

clustree(smc.integrated, prefix = "integrated_snn_res.",
         node_colour = "sex", node_colour_aggr = "pct.female",assay="RNA")

clustree(smc.integrated, prefix = "integrated_snn_res.",
         node_colour = "sex", node_colour_aggr = "pct.male",assay="RNA")

clustree(smc.integrated, prefix = "integrated_snn_res.",
         node_colour = "orig.ident", node_colour_aggr = "pct.fetal",assay="RNA")

clustree(smc.integrated, prefix = "integrated_snn_res.",
         node_colour = "orig.ident", node_colour_aggr = "pct.young",assay="RNA")

clustree(smc.integrated, prefix = "integrated_snn_res.",
         node_colour = "orig.ident", node_colour_aggr = "pct.adult",assay="RNA")

Save Seurat object

DefaultAssay(smc.integrated) <- "RNA"
Idents(smc.integrated) <- smc.integrated$integrated_snn_res.0.1
saveRDS(smc.integrated,file="./output/RDataObjects/smc-int-FYA-filtered.Rds")
#smc.integrated <- readRDS(file="./output/RDataObjects/smc-int-FYA.Rds")
# Load unfiltered counts matrix for every sample (object all)
load("./output/RDataObjects/all-counts.Rdata")

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
 [1] splines   parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] dplyr_1.0.2                 clustree_0.4.3             
 [3] ggraph_2.0.4                NMF_0.23.0                 
 [5] cluster_2.1.0               rngtools_1.5               
 [7] pkgmaker_0.32.2             registry_0.5-1             
 [9] scran_1.18.1                SingleCellExperiment_1.12.0
[11] SummarizedExperiment_1.20.0 GenomicRanges_1.42.0       
[13] GenomeInfoDb_1.26.1         DelayedArray_0.16.0        
[15] MatrixGenerics_1.2.0        matrixStats_0.57.0         
[17] cowplot_1.1.0               monocle_2.18.0             
[19] DDRTree_0.1.5               irlba_2.3.3                
[21] VGAM_1.1-4                  ggplot2_3.3.2              
[23] Matrix_1.2-18               Seurat_3.2.2               
[25] org.Hs.eg.db_3.12.0         AnnotationDbi_1.52.0       
[27] IRanges_2.24.0              S4Vectors_0.28.0           
[29] Biobase_2.50.0              BiocGenerics_0.36.0        
[31] RColorBrewer_1.1-2          edgeR_3.32.0               
[33] limma_3.46.0                workflowr_1.6.2            

loaded via a namespace (and not attached):
  [1] reticulate_1.18           tidyselect_1.1.0         
  [3] RSQLite_2.2.1             htmlwidgets_1.5.2        
  [5] grid_4.0.2                combinat_0.0-8           
  [7] docopt_0.7.1              BiocParallel_1.24.1      
  [9] Rtsne_0.15                munsell_0.5.0            
 [11] codetools_0.2-18          ica_1.0-2                
 [13] statmod_1.4.35            future_1.20.1            
 [15] miniUI_0.1.1.1            withr_2.3.0              
 [17] colorspace_2.0-0          fastICA_1.2-2            
 [19] knitr_1.30                rstudioapi_0.13          
 [21] ROCR_1.0-11               tensor_1.5               
 [23] listenv_0.8.0             labeling_0.4.2           
 [25] git2r_0.27.1              slam_0.1-47              
 [27] GenomeInfoDbData_1.2.4    polyclip_1.10-0          
 [29] farver_2.0.3              bit64_4.0.5              
 [31] pheatmap_1.0.12           rprojroot_2.0.2          
 [33] parallelly_1.21.0         vctrs_0.3.5              
 [35] generics_0.1.0            xfun_0.19                
 [37] R6_2.5.0                  doParallel_1.0.16        
 [39] graphlayouts_0.7.1        rsvd_1.0.3               
 [41] locfit_1.5-9.4            bitops_1.0-6             
 [43] spatstat.utils_1.17-0     assertthat_0.2.1         
 [45] promises_1.1.1            scales_1.1.1             
 [47] gtable_0.3.0              beachmat_2.6.2           
 [49] globals_0.14.0            goftest_1.2-2            
 [51] tidygraph_1.2.0           rlang_0.4.9              
 [53] lazyeval_0.2.2            checkmate_2.0.0          
 [55] yaml_2.2.1                reshape2_1.4.4           
 [57] abind_1.4-5               backports_1.2.0          
 [59] httpuv_1.5.4              tools_4.0.2              
 [61] gridBase_0.4-7            ellipsis_0.3.1           
 [63] ggridges_0.5.2            Rcpp_1.0.5               
 [65] plyr_1.8.6                sparseMatrixStats_1.2.0  
 [67] zlibbioc_1.36.0           purrr_0.3.4              
 [69] RCurl_1.98-1.2            densityClust_0.3         
 [71] rpart_4.1-15              deldir_0.2-3             
 [73] pbapply_1.4-3             viridis_0.5.1            
 [75] zoo_1.8-8                 ggrepel_0.8.2            
 [77] fs_1.5.0                  magrittr_2.0.1           
 [79] data.table_1.13.2         lmtest_0.9-38            
 [81] RANN_2.6.1                whisker_0.4              
 [83] fitdistrplus_1.1-1        patchwork_1.1.0          
 [85] mime_0.9                  evaluate_0.14            
 [87] xtable_1.8-4              sparsesvd_0.2            
 [89] gridExtra_2.3             HSMMSingleCell_1.10.0    
 [91] compiler_4.0.2            tibble_3.0.4             
 [93] KernSmooth_2.23-18        crayon_1.3.4             
 [95] htmltools_0.5.0           mgcv_1.8-33              
 [97] later_1.1.0.1             tidyr_1.1.2              
 [99] DBI_1.1.0                 tweenr_1.0.1             
[101] MASS_7.3-53               igraph_1.2.6             
[103] pkgconfig_2.0.3           plotly_4.9.2.1           
[105] scuttle_1.0.3             foreach_1.5.1            
[107] dqrng_0.2.1               XVector_0.30.0           
[109] stringr_1.4.0             digest_0.6.27            
[111] sctransform_0.3.1         RcppAnnoy_0.0.17         
[113] spatstat.data_1.5-2       rmarkdown_2.5            
[115] leiden_0.3.5              uwot_0.1.9               
[117] DelayedMatrixStats_1.12.1 shiny_1.5.0              
[119] lifecycle_0.2.0           nlme_3.1-150             
[121] jsonlite_1.7.1            BiocNeighbors_1.8.1      
[123] viridisLite_0.3.0         pillar_1.4.7             
[125] lattice_0.20-41           fastmap_1.0.1            
[127] httr_1.4.2                survival_3.2-7           
[129] glue_1.4.2                qlcMatrix_0.9.7          
[131] FNN_1.1.3                 spatstat_1.64-1          
[133] png_0.1-7                 iterators_1.0.13         
[135] bluster_1.0.0             bit_4.0.4                
[137] ggforce_0.3.2             stringi_1.5.3            
[139] blob_1.2.1                BiocSingular_1.6.0       
[141] memoise_1.1.0             future.apply_1.6.0