NSCLC and BRCA CAFs
Chrysa Papadopoulou
Last updated: 2024-09-23
Checks: 7 0
Knit directory: CCL19_FRCs_lung_cancer/
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Load packages
suppressPackageStartupMessages({
library(here)
library(purrr)
library(dplyr)
library(stringr)
library(patchwork)
library(Seurat)
library(Matrix)
library(dittoSeq)
library(gridExtra)
library(gsubfn)
library(ggsci)
library(bigmds)
library(tidyverse)
})Comparison between NSCLC CCL19⁺ FRCs, NSCLC CCL19⁺ CAFs and BRCA CAFs
NSCLC CCL19⁺ FRCs and NSCLC CCL19⁺ CAFs
Set directory
basedir <- here()Read CCL19 FRC data
NSCLC_CCL19_data <- readRDS(paste0(basedir,"/data/Human/NSCLC_CCL19_FRCs_CAFs.rds"))Read NSCLC CCL19⁺ TRC PRC data
NSCLC_CCL19_TRC_PRC <- readRDS(paste0(basedir,"/data/Human/NSCLC_CCL19_TRC_PRC_CAFs.rds"))Define color palette
palet <- c("#1B9E77", "#54B0E4","#E3BE00", "#E41A1C")
names(palet) <- c("CAF2/TRC","CAF1/PRC","AdvFB" ,"SMC/PC")Dotplot with apCAF, iCAF and myCAF gene signatures (Supplementary Figure 3C)
data_conv <-NSCLC_CCL19_TRC_PRC
data_conv <-Remove_ensebl_id(data_conv)
CAF_subsets <- list("iCAF genes"= c("EFEMP1","IL6","C3","CFD","CLU","CXCL12","TNXB",
"HAS1","PLA2G2A","GSN","PCOLCE2","CD34","LEPR",
"CXCL14","CCL2","ADH1B","GPC3","VCAM1","TNC","ALDH1A2"),
"apCAF genes" = c("CD74","HLA-DRB1","HLA-DRA","HLA-DQB1"),
"myCAF genes"=c("FAP","POSTN","LRRC15","MMP11","COL10A1","COMP","COL8A1","GREM1","SULF1","COL13A1",
"COL5A2","LRRC17","COL12A1","THBS2","GJB2","ACTA2","MYH11","ACTG2","DES","COL4A6","BCAM",
"RGS5","MCAM","COL4A1","COL18A1","LAMC3","ARHGDIB"))
DotPlot(object = data_conv, features=CAF_subsets,group.by = "cell_type" ,scale=FALSE,dot.scale = 4) + theme(strip.placement = "outside") +
theme(axis.text.x = element_text(angle = 90,hjust = 1,colour = NULL,face="bold"),axis.title.x.top=element_text(hjust = 1,face="bold")) +xlab(" ")+ylab(" ")
CAF Signatures (Supplementary Figure 3D)
apCAF signature
apCAF_genes <-c("CD74","HLA-DRB1","HLA-DRA","HLA-DQB1")
#Get full gene name (together with the ensembl id)
apCAF_genes <- unlist(lapply(apCAF_genes, function(x) {
get_full_gene_name(x,NSCLC_CCL19_data)
}))
slot_type <-"data"
gn <- "apCAF"
Visualize_GeneSignatures_sc(NSCLC_CCL19_data, apCAF_genes, slot_type, 'average.mean',gn) + ggtitle("apCAF signature")
iCAF signature
iCAF_genes <-c("EFEMP1","IL6","C3","CFD","CLU","CXCL12","TNXB","HAS1","PLA2G2A","GSN","PCOLCE2","CD34","LEPR","CXCL14","CCL2","ADH1B","GPC3","VCAM1","TNC","ALDH1A2")
#Get full gene name (together with the ensembl id)
iCAF_genes <- unlist(lapply(iCAF_genes, function(x) {
get_full_gene_name(x,NSCLC_CCL19_data)
}))
slot_type <-"data"
gn <- "iCAF"
Visualize_GeneSignatures_sc(NSCLC_CCL19_data, iCAF_genes, slot_type, 'average.mean',gn) + ggtitle("iCAF signature")
myCAF signature
myCAF_genes <-c("FAP","POSTN","LRRC15","Mmp11","COL10A1","COMP","COL8A1","GREM1","SULF1","COL13A1","COL5A2","LRRC17","COL12A1","Thbs2","GJB2","ACTA2","MYH11","ACTG2","DES","COL4A6","BCAM","RGS5","MCAM","COL4A1","COL18A1","LAMC3","ARHGDIB")
#Get full gene name (together with the ensembl id)
myCAF_genes <- unlist(lapply(myCAF_genes, function(x) {
get_full_gene_name(x,NSCLC_CCL19_data)
}))
slot_type <-"data"
gn <- "myCAF"
Visualize_GeneSignatures_sc(NSCLC_CCL19_data, myCAF_genes, slot_type, 'average.mean',gn) + ggtitle("myCAF signature")
Session info
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.9
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.2 forcats_1.0.0 readr_2.1.4 tidyverse_2.0.0
[5] bigmds_3.0.0 ggsci_3.0.0 gsubfn_0.7 proto_1.0.0
[9] gridExtra_2.3 dittoSeq_1.12.1 ggplot2_3.4.2 Matrix_1.6-0
[13] SeuratObject_4.1.3 Seurat_4.3.0.1 patchwork_1.1.2 stringr_1.5.0
[17] dplyr_1.1.2 purrr_1.0.1 here_1.0.1 magrittr_2.0.3
[21] circlize_0.4.15 tidyr_1.3.0 tibble_3.2.1 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.1
[3] later_1.3.1 bitops_1.0-7
[5] polyclip_1.10-4 lifecycle_1.0.3
[7] tcltk_4.3.1 rprojroot_2.0.3
[9] globals_0.16.2 processx_3.8.2
[11] lattice_0.21-8 MASS_7.3-60
[13] plotly_4.10.2 sass_0.4.7
[15] rmarkdown_2.23 jquerylib_0.1.4
[17] yaml_2.3.7 httpuv_1.6.11
[19] sctransform_0.3.5 sp_2.0-0
[21] spatstat.sparse_3.0-2 reticulate_1.36.1
[23] cowplot_1.1.1 pbapply_1.7-2
[25] RColorBrewer_1.1-3 abind_1.4-5
[27] zlibbioc_1.46.0 Rtsne_0.16
[29] GenomicRanges_1.52.0 BiocGenerics_0.46.0
[31] RCurl_1.98-1.12 pracma_2.4.4
[33] git2r_0.33.0 GenomeInfoDbData_1.2.10
[35] IRanges_2.34.1 S4Vectors_0.38.1
[37] ggrepel_0.9.3 svd_0.5.5
[39] irlba_2.3.5.1 listenv_0.9.0
[41] spatstat.utils_3.1-0 pheatmap_1.0.12
[43] goftest_1.2-3 spatstat.random_3.1-5
[45] fitdistrplus_1.1-11 parallelly_1.36.0
[47] leiden_0.4.3 codetools_0.2-19
[49] DelayedArray_0.28.0 tidyselect_1.2.0
[51] shape_1.4.6 farver_2.1.1
[53] matrixStats_1.0.0 stats4_4.3.1
[55] spatstat.explore_3.2-1 jsonlite_1.8.7
[57] ellipsis_0.3.2 progressr_0.13.0
[59] ggridges_0.5.4 survival_3.5-5
[61] systemfonts_1.0.4 tools_4.3.1
[63] ragg_1.2.5 ica_1.0-3
[65] Rcpp_1.0.11 glue_1.6.2
[67] SparseArray_1.2.4 xfun_0.39
[69] MatrixGenerics_1.12.3 GenomeInfoDb_1.36.1
[71] withr_2.5.0 fastmap_1.1.1
[73] fansi_1.0.4 callr_3.7.3
[75] digest_0.6.33 timechange_0.2.0
[77] R6_2.5.1 mime_0.12
[79] textshaping_0.3.6 colorspace_2.1-0
[81] scattermore_1.2 tensor_1.5
[83] spatstat.data_3.0-1 utf8_1.2.3
[85] generics_0.1.3 data.table_1.14.8
[87] httr_1.4.6 htmlwidgets_1.6.2
[89] S4Arrays_1.2.1 whisker_0.4.1
[91] uwot_0.1.16 pkgconfig_2.0.3
[93] gtable_0.3.3 lmtest_0.9-40
[95] SingleCellExperiment_1.22.0 XVector_0.40.0
[97] htmltools_0.5.5 scales_1.2.1
[99] Biobase_2.60.0 png_0.1-8
[101] knitr_1.43 rstudioapi_0.15.0
[103] tzdb_0.4.0 reshape2_1.4.4
[105] nlme_3.1-162 cachem_1.0.8
[107] zoo_1.8-12 GlobalOptions_0.1.2
[109] KernSmooth_2.23-22 parallel_4.3.1
[111] miniUI_0.1.1.1 pillar_1.9.0
[113] grid_4.3.1 vctrs_0.6.3
[115] RANN_2.6.1 promises_1.2.0.1
[117] xtable_1.8-4 cluster_2.1.4
[119] evaluate_0.21 cli_3.6.1
[121] compiler_4.3.1 rlang_1.1.1
[123] crayon_1.5.2 future.apply_1.11.0
[125] labeling_0.4.2 ps_1.7.5
[127] getPass_0.2-4 plyr_1.8.8
[129] fs_1.6.3 stringi_1.7.12
[131] viridisLite_0.4.2 deldir_1.0-9
[133] munsell_0.5.0 lazyeval_0.2.2
[135] spatstat.geom_3.2-4 hms_1.1.3
[137] future_1.33.0 shiny_1.7.4.1
[139] highr_0.10 SummarizedExperiment_1.30.2
[141] ROCR_1.0-11 igraph_1.5.0.1
[143] bslib_0.5.0 date()[1] "Mon Sep 23 14:57:25 2024"
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.9
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.2 forcats_1.0.0 readr_2.1.4 tidyverse_2.0.0
[5] bigmds_3.0.0 ggsci_3.0.0 gsubfn_0.7 proto_1.0.0
[9] gridExtra_2.3 dittoSeq_1.12.1 ggplot2_3.4.2 Matrix_1.6-0
[13] SeuratObject_4.1.3 Seurat_4.3.0.1 patchwork_1.1.2 stringr_1.5.0
[17] dplyr_1.1.2 purrr_1.0.1 here_1.0.1 magrittr_2.0.3
[21] circlize_0.4.15 tidyr_1.3.0 tibble_3.2.1 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.1
[3] later_1.3.1 bitops_1.0-7
[5] polyclip_1.10-4 lifecycle_1.0.3
[7] tcltk_4.3.1 rprojroot_2.0.3
[9] globals_0.16.2 processx_3.8.2
[11] lattice_0.21-8 MASS_7.3-60
[13] plotly_4.10.2 sass_0.4.7
[15] rmarkdown_2.23 jquerylib_0.1.4
[17] yaml_2.3.7 httpuv_1.6.11
[19] sctransform_0.3.5 sp_2.0-0
[21] spatstat.sparse_3.0-2 reticulate_1.36.1
[23] cowplot_1.1.1 pbapply_1.7-2
[25] RColorBrewer_1.1-3 abind_1.4-5
[27] zlibbioc_1.46.0 Rtsne_0.16
[29] GenomicRanges_1.52.0 BiocGenerics_0.46.0
[31] RCurl_1.98-1.12 pracma_2.4.4
[33] git2r_0.33.0 GenomeInfoDbData_1.2.10
[35] IRanges_2.34.1 S4Vectors_0.38.1
[37] ggrepel_0.9.3 svd_0.5.5
[39] irlba_2.3.5.1 listenv_0.9.0
[41] spatstat.utils_3.1-0 pheatmap_1.0.12
[43] goftest_1.2-3 spatstat.random_3.1-5
[45] fitdistrplus_1.1-11 parallelly_1.36.0
[47] leiden_0.4.3 codetools_0.2-19
[49] DelayedArray_0.28.0 tidyselect_1.2.0
[51] shape_1.4.6 farver_2.1.1
[53] matrixStats_1.0.0 stats4_4.3.1
[55] spatstat.explore_3.2-1 jsonlite_1.8.7
[57] ellipsis_0.3.2 progressr_0.13.0
[59] ggridges_0.5.4 survival_3.5-5
[61] systemfonts_1.0.4 tools_4.3.1
[63] ragg_1.2.5 ica_1.0-3
[65] Rcpp_1.0.11 glue_1.6.2
[67] SparseArray_1.2.4 xfun_0.39
[69] MatrixGenerics_1.12.3 GenomeInfoDb_1.36.1
[71] withr_2.5.0 fastmap_1.1.1
[73] fansi_1.0.4 callr_3.7.3
[75] digest_0.6.33 timechange_0.2.0
[77] R6_2.5.1 mime_0.12
[79] textshaping_0.3.6 colorspace_2.1-0
[81] scattermore_1.2 tensor_1.5
[83] spatstat.data_3.0-1 utf8_1.2.3
[85] generics_0.1.3 data.table_1.14.8
[87] httr_1.4.6 htmlwidgets_1.6.2
[89] S4Arrays_1.2.1 whisker_0.4.1
[91] uwot_0.1.16 pkgconfig_2.0.3
[93] gtable_0.3.3 lmtest_0.9-40
[95] SingleCellExperiment_1.22.0 XVector_0.40.0
[97] htmltools_0.5.5 scales_1.2.1
[99] Biobase_2.60.0 png_0.1-8
[101] knitr_1.43 rstudioapi_0.15.0
[103] tzdb_0.4.0 reshape2_1.4.4
[105] nlme_3.1-162 cachem_1.0.8
[107] zoo_1.8-12 GlobalOptions_0.1.2
[109] KernSmooth_2.23-22 parallel_4.3.1
[111] miniUI_0.1.1.1 pillar_1.9.0
[113] grid_4.3.1 vctrs_0.6.3
[115] RANN_2.6.1 promises_1.2.0.1
[117] xtable_1.8-4 cluster_2.1.4
[119] evaluate_0.21 cli_3.6.1
[121] compiler_4.3.1 rlang_1.1.1
[123] crayon_1.5.2 future.apply_1.11.0
[125] labeling_0.4.2 ps_1.7.5
[127] getPass_0.2-4 plyr_1.8.8
[129] fs_1.6.3 stringi_1.7.12
[131] viridisLite_0.4.2 deldir_1.0-9
[133] munsell_0.5.0 lazyeval_0.2.2
[135] spatstat.geom_3.2-4 hms_1.1.3
[137] future_1.33.0 shiny_1.7.4.1
[139] highr_0.10 SummarizedExperiment_1.30.2
[141] ROCR_1.0-11 igraph_1.5.0.1
[143] bslib_0.5.0