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integration.R
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integration.R
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library(Seurat)
library(RColorBrewer)
library(SeuratDisk)
pbmc <- readRDS("/home/jxx/MPL/nu16836.rds")
pbmc$cluster_17E=Idents(pbmc)
Idents(pbmc)="cluster_17E"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI")) <- "21"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII")) <- "20"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII Precursor")) <- "19"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT")) <- "17"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT Precursor")) <- "17"
Idents(pbmc, cells = WhichCells(pbmc,idents = "Glycogen Cells")) <- "16"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 2")) <- "14-15"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 1")) <- "14-15"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC")) <- "9"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC Precursor")) <- "6-7-8"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI Precursor")) <- "4-5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP 2")) <- "3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP")) <- "2"
pbmc$cluster_21=Idents(pbmc)
Idents(pbmc)="cluster_17E"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI")) <- "21 SynTI"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII")) <- "20 SynTII"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII Precursor")) <- "19 SynTII Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT")) <- "17 SpA-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT Precursor")) <- "17 SpA-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "Glycogen Cells")) <- "16 Gly-T"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 2")) <- "14-15 SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 1")) <- "14-15 SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC")) <- "9 S-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC Precursor")) <- "6-7-8 S-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI Precursor")) <- "4-5 SynTI Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP 2")) <- "3 LaTP 2"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP")) <- "2 LaTP"
pbmc$type_21=Idents(pbmc)
Idents(pbmc)='GA'
table(Idents(pbmc))
new.cluster.ids <- c("E09.5n","E10.5n",'E12.5n','E14.5n')
names(x = new.cluster.ids) <- levels(x = pbmc)
pbmc <- RenameIdents(object = pbmc, new.cluster.ids, reorder.numeric = T)
table(Idents(pbmc))
pbmc$stage=Idents(pbmc)
pbmc$sample=Idents(pbmc)
nuclei <- CreateSeuratObject(pbmc$RNA@counts, meta.data = pbmc@meta.data, min.cells = 3);nuclei
pbmc <- readRDS("MTR15682.rds");pbmc
cells <- CreateSeuratObject(pbmc$RNA@counts, meta.data = pbmc@meta.data, min.cells = 3);cells
pbmc <- LoadH5Seurat("/sdb/jxx/MTR/V3MTR8067.h5Seurat");pbmc
Idents(pbmc)="stage"
new.cluster.ids <- c('E07.5v3','E08.5v3',"E09.5v3",'E11.5v3', 'E13.5v3')
names(x = new.cluster.ids) <- levels(x = pbmc)
pbmc <- RenameIdents(object = pbmc, new.cluster.ids, reorder.numeric = T)
pbmc$stage=Idents(pbmc)
pbmc$sample=Idents(pbmc)
v3 <- CreateSeuratObject(pbmc$RNA@counts, meta.data = pbmc@meta.data, min.cells = 3);v3
nuclei$origin="Nuclei"
cells$origin="Cells"
v3$origin="v3"
pbmc <- merge(x =cells, y =c(nuclei,v3) , project = "MTR")
pbmc;table(pbmc$origin)
strn=rownames(nuclei)
strc=rownames(cells)
strv3=rownames(v3)
str=intersect(intersect(strn,strc),strv3);length(str);head(str)
count=(pbmc$RNA@counts[str,]);dim(count)
pbmc <- CreateSeuratObject(count, meta.data = pbmc@meta.data, min.cells = 3, project = "MTR");pbmc
pbmc <- NormalizeData(pbmc)
pbmc <- FindVariableFeatures(pbmc, selection.method = 'mean.var.plot', mean.cutoff = c(0.0125, 5), dispersion.cutoff = c(0.5, Inf))
length(x = VariableFeatures(pbmc))
pancreas=pbmc
pancreas.list <- SplitObject(object = pancreas, split.by = "stage")
pancreas.anchors <- FindIntegrationAnchors(object.list = pancreas.list, anchor.features = 8000, dims = 1:30)
pancreas.integrated <- IntegrateData(anchorset = pancreas.anchors, dims = 1:30)
DefaultAssay(object = pancreas.integrated) <- "integrated"
pancreas.integrated <- ScaleData(object = pancreas.integrated)
pancreas.integrated <- RunPCA(object = pancreas.integrated, npcs = 30, verbose = FALSE)
DimPlot(pancreas.integrated); ElbowPlot(pancreas.integrated)
pbmc <- RunUMAP(pancreas.integrated, reduction = "pca", dims = 1:12,verbose=F)
DimPlot(pbmc, label=T)
Idents(pbmc)="cluster_17E"
Idents(pbmc, cells = WhichCells(pbmc,idents = "P3")) <- "P1-2-3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "P2")) <- "P1-2-3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "P1")) <- "P1-2-3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E2")) <- "E2"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E1")) <- "E1"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT")) <- "17"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT Precursor")) <- "17"
Idents(pbmc, cells = WhichCells(pbmc,idents = "Glycogen Cells")) <- "16"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 2")) <- "14-15"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 1")) <- "14-15"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC")) <- "9"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC Precursor")) <- "6-7-8"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI")) <- "21"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII")) <- "20"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI Precursor")) <- "4-5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP 2")) <- "3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII Precursor")) <- "19"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP")) <- "2"
Idents(pbmc, cells = WhichCells(pbmc,idents = "19")) <- "19"
Idents(pbmc, cells = WhichCells(pbmc,idents = "18")) <- "18"
Idents(pbmc, cells = WhichCells(pbmc,idents = "17")) <- "17"
Idents(pbmc, cells = WhichCells(pbmc,idents = "16")) <- "16"
Idents(pbmc, cells = WhichCells(pbmc,idents = "15")) <- "14-15"
Idents(pbmc, cells = WhichCells(pbmc,idents = "14")) <- "14-15"
Idents(pbmc, cells = WhichCells(pbmc,idents = "12")) <- "12"
Idents(pbmc, cells = WhichCells(pbmc,idents = "11")) <- "11"
Idents(pbmc, cells = WhichCells(pbmc,idents = "10")) <- "10"
Idents(pbmc, cells = WhichCells(pbmc,idents = "9")) <- "9"
Idents(pbmc, cells = WhichCells(pbmc,idents = "8")) <- "6-7-8"
Idents(pbmc, cells = WhichCells(pbmc,idents = "7")) <- "6-7-8"
Idents(pbmc, cells = WhichCells(pbmc,idents = "6")) <- "6-7-8"
Idents(pbmc, cells = WhichCells(pbmc,idents = "5")) <- "4-5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "4")) <- "4-5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "3")) <- "3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "2")) <- "2"
Idents(pbmc, cells = WhichCells(pbmc,idents = "1")) <- "1"
pbmc$cluster_21=Idents(pbmc)
Idents(pbmc)="cluster_17E"
Idents(pbmc, cells = WhichCells(pbmc,idents = "P3")) <- "P1-2-3 Biopotential progenitor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "P2")) <- "P1-2-3 Biopotential progenitor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "P1")) <- "P1-2-3 Biopotential progenitor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E2")) <- "E2 The progenitor of S-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E1")) <- "E1 The progenitor of SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT")) <- "17 SpA-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SpT Precursor")) <- "17 SpA-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "Glycogen Cells")) <- "16 Gly-T"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 2")) <- "14-15 SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "JZP 1")) <- "14-15 SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC")) <- "9 S-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "S-TGC Precursor")) <- "6-7-8 S-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI")) <- "21 SynTI"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII")) <- "20 SynTII"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTI Precursor")) <- "4-5 SynTI Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP 2")) <- "3 LaTP 2"
Idents(pbmc, cells = WhichCells(pbmc,idents = "SynTII Precursor")) <- "19 SynTII Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "LaTP")) <- "2 LaTP"
Idents(pbmc, cells = WhichCells(pbmc,idents = "19")) <- "19 SynTII Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "18")) <- "18 EPC Migratory Cell"
Idents(pbmc, cells = WhichCells(pbmc,idents = "17")) <- "17 SpA-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "16")) <- "16 Gly-T"
Idents(pbmc, cells = WhichCells(pbmc,idents = "15")) <- "14-15 SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "14")) <- "14-15 SpT"
Idents(pbmc, cells = WhichCells(pbmc,idents = "12")) <- "12 Secondary P-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "11")) <- "11 Secondary P-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "10")) <- "10 Primary P-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "9")) <- "9 S-TGC"
Idents(pbmc, cells = WhichCells(pbmc,idents = "8")) <- "6-7-8 S-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "7")) <- "6-7-8 S-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "6")) <- "6-7-8 S-TGC Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "5")) <- "4-5 SynTI Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "4")) <- "4-5 SynTI Precursor"
Idents(pbmc, cells = WhichCells(pbmc,idents = "3")) <- "3 LaTP 2"
Idents(pbmc, cells = WhichCells(pbmc,idents = "2")) <- "2 LaTP"
Idents(pbmc, cells = WhichCells(pbmc,idents = "1")) <- "1 TSC and ExE cell"
pbmc$type_21=Idents(pbmc)
C21=colorRampPalette(brewer.pal(12, "Paired"))(30)[c(1:4,7,9,22:24,12:14,27,30,29,5,15,10,18)]
Idents(pbmc)="origin"
new.cluster.ids <- c('Cells_V2','Nuclei_V3','Cells_V3')
names(x = new.cluster.ids) <- levels(x = pbmc)
pbmc <- RenameIdents(object = pbmc, new.cluster.ids, reorder.numeric = T)
Idents(pbmc, cells = WhichCells(pbmc,idents = "Cells_V3")) <- "Cells_V3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "Cells_V2")) <- "Cells_V2"
pbmc$origin=Idents(pbmc)
table(Idents(pbmc))
Idents(pbmc)='cluster_21'
DimPlot(pbmc, label=T,split.by="origin",cols=C21)
Idents(pbmc)='sample'
Idents(pbmc, cells = WhichCells(pbmc,idents = "E13.5v3")) <- "E13.5v3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E13.5")) <- "E13.5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E12.5n")) <- "E12.5n"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E12.5h")) <- "E12.5h"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E12.5")) <- "E12.5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E11.5v3")) <- "E11.5v3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E11.5h")) <- "E11.5h"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E10.5n")) <- "E10.5n"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E10.5h")) <- "E10.5h"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E10.5")) <- "E10.5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E09.5n")) <- "E9.5n"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E09.5v3")) <- "E9.5v3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E09.5")) <- "E9.5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E08.5v3")) <- "E8.5v3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E08.5")) <- "E8.5"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E07.5v3")) <- "E7.5v3"
Idents(pbmc, cells = WhichCells(pbmc,idents = "E07.5")) <- "E7.5"
DimPlot(pbmc, label=F,cols=colorRampPalette(rainbow(9)[c(4,3,6,7,2,1,9,8)])(19))
session_info()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratDisk_0.0.0.9013 RColorBrewer_1.1-2 Seurat_3.1.5
loaded via a namespace (and not attached):
[1] tsne_0.1-3 nlme_3.1-139 bitops_1.0-6
[4] bit64_0.9-7 RcppAnnoy_0.0.14 httr_1.4.2
[7] repr_1.1.4.9000 sctransform_0.2.1 tools_3.6.0
[10] utf8_1.1.4 R6_2.4.1 irlba_2.3.3
[13] KernSmooth_2.23-15 uwot_0.1.8 DBI_1.1.0
[16] lazyeval_0.2.2 colorspace_1.4-1 withr_2.5.0
[19] npsurv_0.4-0 gridExtra_2.3 tidyselect_1.1.2
[22] bit_4.0.4 compiler_3.6.0 cli_3.2.0
[25] hdf5r_1.3.1 plotly_4.9.2 labeling_0.3
[28] caTools_1.18.0 scales_1.1.0 lmtest_0.9-37
[31] ggridges_0.5.2 pbapply_1.4-2 pbdZMQ_0.3-3
[34] stringr_1.4.0 digest_0.6.24 base64enc_0.1-3
[37] pkgconfig_2.0.3 htmltools_0.4.0 htmlwidgets_1.5.1
[40] rlang_1.0.2 farver_2.0.3 generics_0.0.2
[43] zoo_1.8-7 jsonlite_1.8.0 ica_1.0-2
[46] gtools_3.8.1 dplyr_1.0.8 magrittr_2.0.3
[49] patchwork_1.0.1 Matrix_1.2-18 Rcpp_1.0.3
[52] IRkernel_1.1 munsell_0.5.0 fansi_0.4.1
[55] ape_5.3 reticulate_1.14 lifecycle_1.0.1
[58] stringi_1.4.5 MASS_7.3-51.4 gplots_3.0.1.2
[61] Rtsne_0.15 plyr_1.8.5 grid_3.6.0
[64] parallel_3.6.0 gdata_2.18.0 listenv_0.8.0
[67] ggrepel_0.8.1 crayon_1.5.1 lattice_0.20-38
[70] IRdisplay_0.7.0 cowplot_1.0.0 splines_3.6.0
[73] pillar_1.7.0 igraph_1.2.4.2 uuid_0.1-4
[76] future.apply_1.4.0 reshape2_1.4.3 codetools_0.2-16
[79] leiden_0.3.5 glue_1.6.2 evaluate_0.14
[82] lsei_1.2-0 data.table_1.14.2 vctrs_0.4.0
[85] png_0.1-7 gtable_0.3.0 RANN_2.6.1
[88] purrr_0.3.4 tidyr_1.2.0 future_1.16.0
[91] assertthat_0.2.1 ggplot2_3.3.3 rsvd_1.0.2
[94] RSpectra_0.16-0 survival_3.1-8 viridisLite_0.3.0
[97] tibble_3.1.6 cluster_2.0.8 globals_0.12.5
[100] fitdistrplus_1.0-14 ellipsis_0.3.2 ROCR_1.0-7