Fig2
Katie Rhodes
4/19/2021
Last updated: 2021-07-05
Checks: 6 1
Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/
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| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/merge.all.SCTwRegressOrigIdent.Harmony.rds | ../output/merge.all.SCTwRegressOrigIdent.Harmony.rds |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2_CleanOrig.pdf | ../output/pdfs/Fig2_CleanOrig.pdf |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.CleanOrig.png | ../output/figs/fig2.CleanOrig.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.MainClust.png | ../output/figs/fig2.MainClust.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2_SeuratClust.pdf | ../output/pdfs/Fig2_SeuratClust.pdf |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.SeuratClust.png | ../output/figs/fig2.SeuratClust.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.DEann.png | ../output/figs/fig2.DEann.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig_EBandCaoOverlap.png | ../output/figs/SuppFig_EBandCaoOverlap.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/SuppFig_CleanOrig_split.pdf | ../output/pdfs/SuppFig_CleanOrig_split.pdf |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig.cleanOrig | ../output/figs/SuppFig.cleanOrig |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/NearestReferenceCell.Cao.hESC.EuclideanDistanceinHarmonySpace.csv | ../output/NearestReferenceCell.Cao.hESC.EuclideanDistanceinHarmonySpace.csv |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.TransferredLabelUMAP.png | ../output/figs/fig2.TransferredLabelUMAP.png |
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 068f5cb | KLRhodes | 2021-07-04 | wflow_publish(c("analysis/CompiledFits_BatchvInd.Rmd", "analysis/DownSamp_NoiseRatio.Rmd", |
library(Seurat)
library(ggplot2)
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionmerge.all<- readRDS("/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/merge.all.SCTwRegressOrigIdent.Harmony.rds" )options(ggrepel.max.overlaps = Inf, ggrepel.force=1000, ggrepel.box.padding=1000, ggrepel.force_pull=0.01, ggrepel.max.iter=100000, ggrepel.max.time=30)#rename reference metadata
cleanNames<- merge.all@meta.data$orig.ident
cleanNames[cleanNames == "Cao.EtAl"]<- "Fetal Reference"
cleanNames[cleanNames == "EB.Pilot"]<- "EB"
cleanNames[cleanNames == "scHCL.EB20"]<- "EB Reference"
cleanNames[cleanNames == "scHCL.hESC"]<- "hESC Reference"
merge.all<- AddMetaData(merge.all,cleanNames, col.name = "cleanOrig")V<- DimPlot(merge.all, group.by = "cleanOrig", label = F, order= c("hESC Reference","EB Reference", "EB","Fetal Reference"))
V
pdf(file = "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2_CleanOrig.pdf")
V
dev.off()png
2 png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.CleanOrig.png", width=7, height=6, units= "in", res=1080)
V
dev.off()png
2 Idents(merge.all)<- "orig.ident"
sub<- subset(merge.all, idents= c("Cao.EtAl", "EB.Pilot"))V<- DimPlot(sub, group.by = "Main_cluster_name", label = T, repel = T, label.size = 2.1)+NoLegend()+theme(aspect.ratio = 1)Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
Please use `as_label()` or `as_name()` instead.
This warning is displayed once per session.V
png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.MainClust.png", width=6, height=6, units= "in", res=1080)
V
dev.off()png
2 V<- DimPlot(sub, group.by = "SCT_snn_res.0.1", label = T, repel = F, label.size = 5)+NoLegend()
V
pdf(file = "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2_SeuratClust.pdf")
V
dev.off()png
2 png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.SeuratClust.png", width=6, height=6, units= "in", res=1080)
V
dev.off()png
2 #rename clusters by DE annotation
DEann<- sub@meta.data$SCT_snn_res.0.1
DEann[DEann == "0"]<- "Pluripotent Cells"
DEann[DEann == "1"]<- "Early Ectoderm"
DEann[DEann == "2"]<- "Mesoderm"
DEann[DEann == "3"]<- "Neural Crest"
DEann[DEann == "4"]<- "Endoderm"
DEann[DEann == "5"]<- "Neurons"
DEann[DEann == "6"]<- "Endothelial Cells"
sub<- AddMetaData(sub,DEann, col.name = "DEann")V<- DimPlot(sub, group.by = "DEann", label = T, repel = F, label.size = 4)+NoLegend()
V
png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.DEann.png", width=6, height=6, units= "in", res=1080)
V
dev.off()png
2 x<- DimPlot(sub, group.by = "cleanOrig", cols = c("#E69F00", "#0072B2"))+NoLegend()
x
z<- DimPlot(sub, group.by = "cleanOrig", order="Cao.EtAl", cols = c("#E69F00", "#0072B2"))
z
xz<- x + z
xz
png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig_EBandCaoOverlap.png", width=6, height=3, units= "in", res=1080)
xz
dev.off()png
2 V<- DimPlot(merge.all, split.by = "cleanOrig", label = F, order= c("hESC Reference","EB Reference", "EB","Fetal Reference"))+NoLegend()
V
pdf(file = "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/SuppFig_CleanOrig_split.pdf")
V
dev.off()png
2 png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig.cleanOrig,split.png", width=8, height=3, units= "in", res=1080)
V
dev.off()png
2 nearest.ann<- read.csv("/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/NearestReferenceCell.Cao.hESC.EuclideanDistanceinHarmonySpace.csv")
sub<- subset(merge.all, idents= c("EB.Pilot"))
EB.cell.id<- rownames(sub@meta.data)
sub@meta.data<- cbind(sub@meta.data, EB.cell.id)
sub@meta.data<- full_join(sub@meta.data, nearest.ann, by= c("EB.cell.id"))
rownames(sub@meta.data)<- EB.cell.idM<- DimPlot(sub, group.by="annotation", pt.size = 0.2, label.size = 2.5,label=T, repel=T) +NoLegend()
M
png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/fig2.TransferredLabelUMAP.png", width=6, height=6, units= "in", res=1080)
M
dev.off()png
2 sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.2 ggplot2_3.3.3 Seurat_3.2.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-0 deldir_0.1-28
[4] ellipsis_0.3.1 ggridges_0.5.2 rprojroot_2.0.2
[7] fs_1.4.2 spatstat.data_1.4-3 farver_2.0.3
[10] leiden_0.3.3 listenv_0.8.0 npsurv_0.4-0
[13] ggrepel_0.9.0 codetools_0.2-16 splines_3.6.1
[16] lsei_1.2-0 knitr_1.29 polyclip_1.10-0
[19] jsonlite_1.7.2 ica_1.0-2 cluster_2.1.0
[22] png_0.1-7 uwot_0.1.10 shiny_1.5.0
[25] sctransform_0.2.1 compiler_3.6.1 httr_1.4.2
[28] Matrix_1.2-18 fastmap_1.0.1 lazyeval_0.2.2
[31] later_1.1.0.1 htmltools_0.5.0 tools_3.6.1
[34] rsvd_1.0.3 igraph_1.2.6 gtable_0.3.0
[37] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4
[40] rappdirs_0.3.3 Rcpp_1.0.6 spatstat_1.64-1
[43] vctrs_0.3.6 gdata_2.18.0 ape_5.4-1
[46] nlme_3.1-140 lmtest_0.9-37 xfun_0.16
[49] stringr_1.4.0 globals_0.12.5 mime_0.9
[52] miniUI_0.1.1.1 lifecycle_0.2.0 irlba_2.3.3
[55] gtools_3.8.2 goftest_1.2-2 future_1.18.0
[58] MASS_7.3-51.4 zoo_1.8-8 scales_1.1.1
[61] promises_1.1.1 spatstat.utils_1.17-0 parallel_3.6.1
[64] RColorBrewer_1.1-2 yaml_2.2.1 reticulate_1.20
[67] pbapply_1.4-2 gridExtra_2.3 rpart_4.1-15
[70] stringi_1.5.3 highr_0.8 caTools_1.18.0
[73] rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-6
[76] evaluate_0.14 lattice_0.20-38 ROCR_1.0-7
[79] purrr_0.3.4 tensor_1.5 labeling_0.4.2
[82] patchwork_1.1.1 htmlwidgets_1.5.1 cowplot_1.1.1
[85] tidyselect_1.1.0 RcppAnnoy_0.0.18 plyr_1.8.6
[88] magrittr_2.0.1 R6_2.5.0 gplots_3.0.4
[91] generics_0.1.0 withr_2.4.2 pillar_1.4.7
[94] whisker_0.4 mgcv_1.8-28 fitdistrplus_1.0-14
[97] survival_3.2-3 abind_1.4-5 tibble_3.0.4
[100] future.apply_1.6.0 crayon_1.3.4 KernSmooth_2.23-15
[103] plotly_4.9.2.1 rmarkdown_2.3 grid_3.6.1
[106] data.table_1.13.4 git2r_0.26.1 digest_0.6.27
[109] xtable_1.8-4 tidyr_1.1.0 httpuv_1.5.4
[112] munsell_0.5.0 viridisLite_0.3.0
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.2 ggplot2_3.3.3 Seurat_3.2.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-0 deldir_0.1-28
[4] ellipsis_0.3.1 ggridges_0.5.2 rprojroot_2.0.2
[7] fs_1.4.2 spatstat.data_1.4-3 farver_2.0.3
[10] leiden_0.3.3 listenv_0.8.0 npsurv_0.4-0
[13] ggrepel_0.9.0 codetools_0.2-16 splines_3.6.1
[16] lsei_1.2-0 knitr_1.29 polyclip_1.10-0
[19] jsonlite_1.7.2 ica_1.0-2 cluster_2.1.0
[22] png_0.1-7 uwot_0.1.10 shiny_1.5.0
[25] sctransform_0.2.1 compiler_3.6.1 httr_1.4.2
[28] Matrix_1.2-18 fastmap_1.0.1 lazyeval_0.2.2
[31] later_1.1.0.1 htmltools_0.5.0 tools_3.6.1
[34] rsvd_1.0.3 igraph_1.2.6 gtable_0.3.0
[37] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4
[40] rappdirs_0.3.3 Rcpp_1.0.6 spatstat_1.64-1
[43] vctrs_0.3.6 gdata_2.18.0 ape_5.4-1
[46] nlme_3.1-140 lmtest_0.9-37 xfun_0.16
[49] stringr_1.4.0 globals_0.12.5 mime_0.9
[52] miniUI_0.1.1.1 lifecycle_0.2.0 irlba_2.3.3
[55] gtools_3.8.2 goftest_1.2-2 future_1.18.0
[58] MASS_7.3-51.4 zoo_1.8-8 scales_1.1.1
[61] promises_1.1.1 spatstat.utils_1.17-0 parallel_3.6.1
[64] RColorBrewer_1.1-2 yaml_2.2.1 reticulate_1.20
[67] pbapply_1.4-2 gridExtra_2.3 rpart_4.1-15
[70] stringi_1.5.3 highr_0.8 caTools_1.18.0
[73] rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-6
[76] evaluate_0.14 lattice_0.20-38 ROCR_1.0-7
[79] purrr_0.3.4 tensor_1.5 labeling_0.4.2
[82] patchwork_1.1.1 htmlwidgets_1.5.1 cowplot_1.1.1
[85] tidyselect_1.1.0 RcppAnnoy_0.0.18 plyr_1.8.6
[88] magrittr_2.0.1 R6_2.5.0 gplots_3.0.4
[91] generics_0.1.0 withr_2.4.2 pillar_1.4.7
[94] whisker_0.4 mgcv_1.8-28 fitdistrplus_1.0-14
[97] survival_3.2-3 abind_1.4-5 tibble_3.0.4
[100] future.apply_1.6.0 crayon_1.3.4 KernSmooth_2.23-15
[103] plotly_4.9.2.1 rmarkdown_2.3 grid_3.6.1
[106] data.table_1.13.4 git2r_0.26.1 digest_0.6.27
[109] xtable_1.8-4 tidyr_1.1.0 httpuv_1.5.4
[112] munsell_0.5.0 viridisLite_0.3.0