Supplementary figure 2
Last updated: 2024-12-24
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Knit directory: proj_distal/analysis/
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## scRNA-seq
library(Seurat)
#packageVersion("Seurat")
# Plotting
library("ggplot2")
library(cowplot)
# Presentation
library("knitr")
# Others
library(stringr)source(here::here("R/00_generalDeps.R"))
source(here::here("R/output.R"))filt_path <- here::here("data/processed/figure2_output_seurat.rds")Introduction
In this document we are going to perform plotting supplementary figure 2 panel A using Seurat.
Loading seurat object processed
if (file.exists(filt_path)) {
sc_seurat <- readRDS(filt_path)
} else {
stop("Supplementary figure 2 dataset is missing. ",
"Please check Input first.",
call. = FALSE)
}visualization
plot metadata
DimPlot( sc_seurat, label=TRUE, label.size = 8) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none") 
clusterName = 7
clusterCells = which( Idents( sc_seurat) == clusterName);
DimPlot( sc_seurat, reduction = "umap",
cols="#44444422",
cells.highlight = clusterCells,
cols.highlight = "#FF000088",
sizes.highlight = 1.5,
order = clusterCells, # Plot highlighted cells last
group.by=NULL) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none") +
ggtitle( paste( "Cluster", clusterName))
featuresName = c("TRBV5-6", "TRAV8-4", "PLEK", "PRF1", "NKG7", "CCL5")
FeaturePlot( sc_seurat, features = featuresName, reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none");
Supplementary figure 2
Panel A
p1 <-DimPlot( sc_seurat, label=TRUE, label.size = 8) + ggtitle("Clusters")+
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
p2 <- DimPlot( sc_seurat, reduction = "umap",
cols="#44444422",
cells.highlight = clusterCells,
cols.highlight = "#FF000088",
sizes.highlight = 1.5,
order = clusterCells, # Plot highlighted cells last
group.by=NULL) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none") +
ggtitle( paste( "Cluster", clusterName))
p3 <- FeaturePlot( sc_seurat, features = featuresName[1], reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
p4 <- FeaturePlot( sc_seurat, features = featuresName[2], reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
p5 <- FeaturePlot( sc_seurat, features = featuresName[3], reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
p6 <- FeaturePlot( sc_seurat, features = featuresName[4], reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
p7 <- FeaturePlot( sc_seurat, features = featuresName[5], reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
p8 <- FeaturePlot( sc_seurat, features = featuresName[6], reduction = "umap", order = TRUE) +
theme( axis.title.x = element_blank(),
axis.title.y = element_blank(),
legend.position = "none")
fig <- plot_grid(p1, p2, p3, p4, p5, p6, p7, p8, nrow = 4, labels = "A")
fig
dir.create(here::here("output", DOCNAME), showWarnings = FALSE)
ggsave(here::here("output", DOCNAME, "suppfigure2-panelA.pdf"), fig,
width = 6, height = 9, scale = 1)
ggsave(here::here("output", DOCNAME, "suppfigure2-panelA.png"), fig,
width = 6, height = 9, scale = 1)Session information
devtools::session_info()─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os Ubuntu 20.04.3 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2024-12-24
pandoc 2.14.0.3 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
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assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.1.0)
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cli 3.6.1 2023-03-23 [1] RSPM (R 4.1.0)
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cowplot * 1.1.1 2020-12-30 [1] RSPM (R 4.1.0)
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here 1.0.1 2020-12-13 [1] RSPM (R 4.1.0)
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jsonlite 1.8.0 2022-02-22 [1] RSPM (R 4.1.0)
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listenv 0.8.0 2019-12-05 [1] RSPM (R 4.1.0)
lmtest 0.9-39 2021-11-07 [1] RSPM (R 4.1.0)
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MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.2)
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[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
──────────────────────────────────────────────────────────────────────────────
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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
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[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] RColorBrewer_1.1-2 scales_1.2.1 ggpubr_0.4.0 rstatix_0.7.0
[5] readxl_1.3.1 stringr_1.4.0 knitr_1.37 cowplot_1.1.1
[9] ggplot2_3.4.4 SeuratObject_4.0.4 Seurat_4.1.0
loaded via a namespace (and not attached):
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[7] splines_4.1.2 listenv_0.8.0 scattermore_0.7
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[13] fansi_1.0.2 memoise_2.0.1 magrittr_2.0.2
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[106] pillar_1.7.0 lifecycle_1.0.3 spatstat.geom_2.4-0
[109] lmtest_0.9-39 jquerylib_0.1.4 RcppAnnoy_0.0.19
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[118] KernSmooth_2.23-20 gridExtra_2.3 parallelly_1.30.0
[121] sessioninfo_1.2.2 codetools_0.2-18 pkgload_1.2.4
[124] MASS_7.3-54 assertthat_0.2.1 rprojroot_2.0.2
[127] withr_2.5.0 sctransform_0.3.3 mgcv_1.8-38
[130] parallel_4.1.2 grid_4.1.2 rpart_4.1-15
[133] tidyr_1.2.0 rmarkdown_2.11 carData_3.0-5
[136] Rtsne_0.15 git2r_0.33.0 shiny_1.7.1