Fig2.5.5New
Katie Rhodes
4/19/2021
Last updated: 2021-12-08
Checks: 6 1
Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/
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| absolute | relative |
|---|---|
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/5newlines.merge.all.SCTwRegressOrigIdent.Harmony.rds | ../output/5newlines.merge.all.SCTwRegressOrigIdent.Harmony.rds |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/5NEWLINES.BroadCellTypeCatAssignment.basedonclustersres0.15.csv | ../output/5NEWLINES.BroadCellTypeCatAssignment.basedonclustersres0.15.csv |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2.5_5New_CleanOrig.pdf | ../output/pdfs/Fig2.5_5New_CleanOrig.pdf |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.CleanOrig.png | ../output/figs/Fig2.5.5New.CleanOrig.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.MainClust.png | ../output/figs/Fig2.5.5New.MainClust.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2.5_5New_SeuratClust.pdf | ../output/pdfs/Fig2.5_5New_SeuratClust.pdf |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.SeuratClust.png | ../output/figs/Fig2.5.5New.SeuratClust.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.DEann.png | ../output/figs/Fig2.5.5New.DEann.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig_5NEWLINES_EBandCaoOverlap.png | ../output/figs/SuppFig_5NEWLINES_EBandCaoOverlap.png |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/SuppFig_5NEWLINES_CleanOrig_split.pdf | ../output/pdfs/SuppFig_5NEWLINES_CleanOrig_split.pdf |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig.5NEWLINES.cleanOrig | ../output/figs/SuppFig.5NEWLINES.cleanOrig |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/5NEWLINES.MostCommonAnnotation.FiveNearestRefCells.csv | ../output/5NEWLINES.MostCommonAnnotation.FiveNearestRefCells.csv |
| /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.TransferredLabelUMAP.png | ../output/figs/Fig2.5.5New.TransferredLabelUMAP.png |
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 094e7ee | KLRhodes | 2021-12-08 | Publish aesthetically updated figs and additional line analyses |
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/5newlines.merge.all.SCTwRegressOrigIdent.Harmony.rds")#Get broad cell type category assignments for 5New lines based on cluster marker genes
PilotAnn<-read.csv("/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/5NEWLINES.BroadCellTypeCatAssignment.basedonclustersres0.15.csv", header=T)
#prep to add metadata
cellid<- as.data.frame(rownames(merge.all@meta.data))
colnames(cellid)<- "cellid"
PilotAnn<- PilotAnn[2:3]
catbyid<- left_join(cellid, PilotAnn, by = c("cellid" ="V1"))
merge.all<- AddMetaData(merge.all, metadata=catbyid$V2, "PilotAnn")options(ggrepel.max.overlaps = Inf, ggrepel.force=1000, ggrepel.box.padding=1000, ggrepel.force_pull=0.01, ggrepel.max.iter=100000, ggrepel.max.time=30)#rename reference metadata
cleanNames<- merge.all@meta.data$orig.ident
cleanNames[cleanNames == "Cao.EtAl"]<- "Fetal Reference"
cleanNames[cleanNames == "EB.5New"]<- "EB Additional Lines"
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 Additional Lines","Fetal Reference")) +NoAxes()
V
pdf(file = "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/pdfs/Fig2.5_5New_CleanOrig.pdf")
V
dev.off()png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.CleanOrig.png", width=7, height=6, units= "in", res=1080)
V
dev.off()Idents(merge.all)<- "orig.ident"
sub<- subset(merge.all, idents= c("Cao.EtAl", "EB.5New"))V<- DimPlot(sub, group.by = "Main_cluster_name", label = T, repel = T, label.size = 2.1)+NoLegend()+theme(aspect.ratio = 1)+ NoAxes()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/Fig2.5.5New.MainClust.png", width=6, height=6, units= "in", res=1080)
V
dev.off()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/Fig2.5_5New_SeuratClust.pdf")
V
dev.off()png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.SeuratClust.png", width=6, height=6, units= "in", res=1080)
V
dev.off()V<- DimPlot(sub, group.by = "PilotAnn", label = T, repel = F, label.size = 4)+NoLegend()+NoAxes()
V
png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.DEann.png", width=6, height=6, units= "in", res=1080)
V
dev.off()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_5NEWLINES_EBandCaoOverlap.png", width=6, height=3, units= "in", res=1080)
xz
dev.off()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_5NEWLINES_CleanOrig_split.pdf")
V
dev.off()png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/SuppFig.5NEWLINES.cleanOrig,split.png", width=8, height=3, units= "in", res=1080)
V
dev.off()nearest.ann<- read.csv("/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/5NEWLINES.MostCommonAnnotation.FiveNearestRefCells.csv")
sub<- subset(merge.all, idents= c("EB.5New"))
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()+NoAxes()
M
png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Fig2.5.5New.TransferredLabelUMAP.png", width=6, height=6, units= "in", res=1080)
M
dev.off()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] 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] dplyr_1.0.2 ggplot2_3.3.5 Seurat_3.2.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] nlme_3.1-140 fs_1.4.2 RcppAnnoy_0.0.18
[4] RColorBrewer_1.1-2 httr_1.4.2 rprojroot_2.0.2
[7] sctransform_0.2.1 tools_3.6.1 utf8_1.2.2
[10] R6_2.5.1 irlba_2.3.3 rpart_4.1-15
[13] KernSmooth_2.23-15 uwot_0.1.10 mgcv_1.8-28
[16] lazyeval_0.2.2 colorspace_2.0-2 withr_2.4.2
[19] npsurv_0.4-0 gridExtra_2.3 tidyselect_1.1.0
[22] compiler_3.6.1 git2r_0.26.1 plotly_4.9.2.1
[25] labeling_0.4.2 scales_1.1.1 spatstat.data_1.4-3
[28] lmtest_0.9-37 ggridges_0.5.2 pbapply_1.4-2
[31] rappdirs_0.3.3 goftest_1.2-2 spatstat_1.64-1
[34] stringr_1.4.0 digest_0.6.28 spatstat.utils_1.17-0
[37] rmarkdown_2.3 pkgconfig_2.0.3 htmltools_0.5.0
[40] fastmap_1.0.1 highr_0.8 htmlwidgets_1.5.1
[43] rlang_0.4.11 shiny_1.5.0 farver_2.1.0
[46] generics_0.1.0 zoo_1.8-8 jsonlite_1.7.2
[49] ica_1.0-2 magrittr_2.0.1 patchwork_1.1.1
[52] Matrix_1.2-18 Rcpp_1.0.6 munsell_0.5.0
[55] fansi_0.5.0 abind_1.4-5 ape_5.4-1
[58] reticulate_1.20 lifecycle_1.0.1 stringi_1.5.3
[61] whisker_0.4 yaml_2.2.1 MASS_7.3-51.4
[64] Rtsne_0.15 plyr_1.8.6 grid_3.6.1
[67] parallel_3.6.1 listenv_0.8.0 promises_1.1.1
[70] ggrepel_0.9.0 crayon_1.4.1 deldir_0.1-28
[73] miniUI_0.1.1.1 lattice_0.20-38 cowplot_1.1.1
[76] splines_3.6.1 tensor_1.5 knitr_1.29
[79] pillar_1.6.3 igraph_1.2.6 reshape2_1.4.4
[82] future.apply_1.6.0 codetools_0.2-16 leiden_0.3.3
[85] glue_1.4.2 evaluate_0.14 lsei_1.2-0
[88] data.table_1.13.4 png_0.1-7 vctrs_0.3.8
[91] httpuv_1.5.4 polyclip_1.10-0 gtable_0.3.0
[94] RANN_2.6.1 purrr_0.3.4 tidyr_1.1.0
[97] future_1.18.0 xfun_0.16 rsvd_1.0.3
[100] mime_0.9 xtable_1.8-4 later_1.1.0.1
[103] survival_3.2-3 viridisLite_0.4.0 tibble_3.1.5
[106] cluster_2.1.0 globals_0.12.5 fitdistrplus_1.0-14
[109] ellipsis_0.3.2 ROCR_1.0-11
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] 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] dplyr_1.0.2 ggplot2_3.3.5 Seurat_3.2.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] nlme_3.1-140 fs_1.4.2 RcppAnnoy_0.0.18
[4] RColorBrewer_1.1-2 httr_1.4.2 rprojroot_2.0.2
[7] sctransform_0.2.1 tools_3.6.1 utf8_1.2.2
[10] R6_2.5.1 irlba_2.3.3 rpart_4.1-15
[13] KernSmooth_2.23-15 uwot_0.1.10 mgcv_1.8-28
[16] lazyeval_0.2.2 colorspace_2.0-2 withr_2.4.2
[19] npsurv_0.4-0 gridExtra_2.3 tidyselect_1.1.0
[22] compiler_3.6.1 git2r_0.26.1 plotly_4.9.2.1
[25] labeling_0.4.2 scales_1.1.1 spatstat.data_1.4-3
[28] lmtest_0.9-37 ggridges_0.5.2 pbapply_1.4-2
[31] rappdirs_0.3.3 goftest_1.2-2 spatstat_1.64-1
[34] stringr_1.4.0 digest_0.6.28 spatstat.utils_1.17-0
[37] rmarkdown_2.3 pkgconfig_2.0.3 htmltools_0.5.0
[40] fastmap_1.0.1 highr_0.8 htmlwidgets_1.5.1
[43] rlang_0.4.11 shiny_1.5.0 farver_2.1.0
[46] generics_0.1.0 zoo_1.8-8 jsonlite_1.7.2
[49] ica_1.0-2 magrittr_2.0.1 patchwork_1.1.1
[52] Matrix_1.2-18 Rcpp_1.0.6 munsell_0.5.0
[55] fansi_0.5.0 abind_1.4-5 ape_5.4-1
[58] reticulate_1.20 lifecycle_1.0.1 stringi_1.5.3
[61] whisker_0.4 yaml_2.2.1 MASS_7.3-51.4
[64] Rtsne_0.15 plyr_1.8.6 grid_3.6.1
[67] parallel_3.6.1 listenv_0.8.0 promises_1.1.1
[70] ggrepel_0.9.0 crayon_1.4.1 deldir_0.1-28
[73] miniUI_0.1.1.1 lattice_0.20-38 cowplot_1.1.1
[76] splines_3.6.1 tensor_1.5 knitr_1.29
[79] pillar_1.6.3 igraph_1.2.6 reshape2_1.4.4
[82] future.apply_1.6.0 codetools_0.2-16 leiden_0.3.3
[85] glue_1.4.2 evaluate_0.14 lsei_1.2-0
[88] data.table_1.13.4 png_0.1-7 vctrs_0.3.8
[91] httpuv_1.5.4 polyclip_1.10-0 gtable_0.3.0
[94] RANN_2.6.1 purrr_0.3.4 tidyr_1.1.0
[97] future_1.18.0 xfun_0.16 rsvd_1.0.3
[100] mime_0.9 xtable_1.8-4 later_1.1.0.1
[103] survival_3.2-3 viridisLite_0.4.0 tibble_3.1.5
[106] cluster_2.1.0 globals_0.12.5 fitdistrplus_1.0-14
[109] ellipsis_0.3.2 ROCR_1.0-11