Last updated: 2021-02-05
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Knit directory: melanoma_publication_old_data/
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Color schemes
knitr::opts_chunk$set(echo = TRUE, message= FALSE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())library(SingleCellExperiment)
library(colorRamps)sce_rna <- readRDS("data/sce_RNA.rds")
sce_prot <- readRDS("data/sce_protein.rds")col <- c("sienna4", "tomato", "gray65", "sienna1", "lightblue", "deepskyblue", "cyan",
"dodgerblue2", "darkolivegreen1", "darkolivegreen4", "darkolivegreen","darkgreen", "yellow2",
"khaki", "gold")
names <- c("Tumor", "Stroma", "unknown", "Vasculature", "Tcell", "Tcytotoxic", "Thelper",
"Tregulatory", "Bcell", "BnTcell", "HLA-DR", "CD38" ,"Macrophage", "Neutrophil", "pDC")
#barplot(seq_along(names), col=col, main="Pastel_hcl", names.arg = names)
col_celltypes <- col
names(col_celltypes) <- namescell_rna <- col_celltypes[c("Tumor", "Stroma", "unknown", "Vasculature", "Tcell",
"Tcytotoxic", "HLA-DR", "CD38","Macrophage", "Neutrophil")]
metadata(sce_rna)$colour_vectors$celltype <- cell_rna# add color vector to metadata
targets <- metadata(sce_rna)$chemokines_morethan600_withcontrol
color_chemo <- primary.colors(length(targets))
names(color_chemo) <- targets
#barplot(seq_along(targets), col=color_chemo, main="Pastel_hcl", names.arg = targets)
metadata(sce_rna)$colour_vectors$chemokine_combinations <- color_chemo
# replace order of chemokines to match order without control samples for upset plot only (ATTENTION! HARD CODED)
new_order <- replace(targets, match(c("CXCL8", "CCL18"),targets), c("CCL18", "CXCL8"))
color_chemo <- color_chemo[new_order]
metadata(sce_rna)$colour_vectors$chemokine_combinations_no_control_UPSETplot <- color_chemocol_vector_chemokines <- metadata(sce_rna)$colour_vector$chemokine_combinations
col_vector_chemokines <- col_vector_chemokines[c("CXCL13", "CXCL10", "CXCL9", "CCL2", "CXCL12", "CCL19", "CCL18", "CXCL8", "CCL4", "CCL22")]
col_vector_new_chemo <- c("forestgreen")
names(col_vector_new_chemo) <- c("CCL8")
col_vector_chemokines <- c(col_vector_chemokines, col_vector_new_chemo)
metadata(sce_rna)$colour_vectors$chemokine_single <- col_vector_chemokinescell_protein <- col_celltypes[c("Tumor", "Stroma", "unknown", "Tcytotoxic",
"Thelper", "Tregulatory", "Bcell", "BnTcell",
"Macrophage", "Neutrophil", "pDC")]
metadata(sce_prot)$colour_vectors$celltype <- cell_proteinsaveRDS(sce_rna, "data/sce_RNA.rds")
saveRDS(sce_prot, "data/sce_protein.rds")
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 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=C
[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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] colorRamps_2.3 SingleCellExperiment_1.12.0
[3] SummarizedExperiment_1.20.0 Biobase_2.50.0
[5] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[7] IRanges_2.24.1 S4Vectors_0.28.1
[9] BiocGenerics_0.36.0 MatrixGenerics_1.2.0
[11] matrixStats_0.57.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 XVector_0.30.0 pillar_1.4.7
[4] compiler_4.0.3 later_1.1.0.1 git2r_0.28.0
[7] zlibbioc_1.36.0 bitops_1.0-6 tools_4.0.3
[10] digest_0.6.27 lattice_0.20-41 evaluate_0.14
[13] lifecycle_0.2.0 tibble_3.0.4 pkgconfig_2.0.3
[16] rlang_0.4.10 Matrix_1.3-2 DelayedArray_0.16.0
[19] rstudioapi_0.13 yaml_2.2.1 xfun_0.20
[22] GenomeInfoDbData_1.2.4 stringr_1.4.0 knitr_1.30
[25] fs_1.5.0 vctrs_0.3.6 grid_4.0.3
[28] rprojroot_2.0.2 glue_1.4.2 R6_2.5.0
[31] rmarkdown_2.6 magrittr_2.0.1 whisker_0.4
[34] promises_1.1.1 ellipsis_0.3.1 htmltools_0.5.0
[37] httpuv_1.5.4 stringi_1.5.3 RCurl_1.98-1.2
[40] crayon_1.3.4