08_coloring
2020-11-25
Last updated: 2022-02-10
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Knit directory: MelanomaIMC/
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| Rmd | 3203891 | toobiwankenobi | 2021-02-19 | change celltype names |
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| Rmd | 2e443a5 | toobiwankenobi | 2021-02-09 | remove files that are not needed |
Introduction
Color schemes
Preparations
knitr::opts_chunk$set(echo = TRUE, message= FALSE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())Load libraries
library(SingleCellExperiment)
library(colorRamps)Load data
sce_rna <- readRDS("data/data_for_analysis/sce_RNA.rds")
sce_prot <- readRDS("data/data_for_analysis/sce_protein.rds")All celltypes
colvec <- c("sienna4", "tomato", "gray65", "red3", "blueviolet", "deeppink", "blueviolet",
"darkorchid1", "deepskyblue", "darkblue", "deepskyblue","aquamarine", "green",
"darkgreen", "yellow")
names(colvec) <- c("Tumor", "Stroma", "unknown", "Vasculature", "CD8- T cell", "CD8+ T cell", "CD4+ T cell",
"FOXP3+ T cell", "B cell", "BnT cell", "HLA-DR", "CD38" ,"Macrophage", "Neutrophil", "pDC")
pie(c(rep(1,length((colvec)))),col = colvec,labels = names(colvec))
col_celltypes <- colvec
names(col_celltypes) <- names(colvec)RNA
Celltypes
cell_rna <- col_celltypes[c("Tumor", "Stroma", "unknown", "Vasculature", "CD8- T cell",
"CD8+ T cell", "HLA-DR", "CD38","Macrophage", "Neutrophil")]
metadata(sce_rna)$colour_vectors$celltype <- cell_rnaChemokines (Combinations)
# 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$chemokine_combinations <- color_chemoChemokines (single)
col_vector_chemokines <- metadata(sce_rna)$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$chemokine_single <- col_vector_chemokinesProtein
Celltypes
cell_protein <- col_celltypes[c("Tumor", "Stroma", "unknown", "CD8+ T cell",
"CD4+ T cell", "FOXP3+ T cell", "B cell", "BnT cell",
"Macrophage", "Neutrophil", "pDC")]
metadata(sce_prot)$colour_vectors$celltype <- cell_proteinSave RDS
saveRDS(sce_rna, "data/data_for_analysis/sce_RNA.rds")
saveRDS(sce_prot, "data/data_for_analysis/sce_protein.rds")
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
[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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] colorRamps_2.3 SingleCellExperiment_1.16.0
[3] SummarizedExperiment_1.24.0 Biobase_2.54.0
[5] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[7] IRanges_2.28.0 S4Vectors_0.32.3
[9] BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[11] matrixStats_0.61.0 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] xfun_0.29 bslib_0.3.1 lattice_0.20-45
[4] vctrs_0.3.8 htmltools_0.5.2 yaml_2.2.2
[7] utf8_1.2.2 rlang_1.0.0 jquerylib_0.1.4
[10] later_1.3.0 pillar_1.7.0 glue_1.6.1
[13] GenomeInfoDbData_1.2.7 lifecycle_1.0.1 stringr_1.4.0
[16] zlibbioc_1.40.0 evaluate_0.14 knitr_1.37
[19] callr_3.7.0 fastmap_1.1.0 httpuv_1.6.5
[22] ps_1.6.0 fansi_1.0.2 highr_0.9
[25] Rcpp_1.0.8 promises_1.2.0.1 DelayedArray_0.20.0
[28] jsonlite_1.7.3 XVector_0.34.0 fs_1.5.2
[31] digest_0.6.29 stringi_1.7.6 processx_3.5.2
[34] getPass_0.2-2 grid_4.1.2 rprojroot_2.0.2
[37] cli_3.1.1 tools_4.1.2 bitops_1.0-7
[40] magrittr_2.0.2 sass_0.4.0 RCurl_1.98-1.5
[43] tibble_3.1.6 crayon_1.4.2 whisker_0.4
[46] pkgconfig_2.0.3 Matrix_1.4-0 ellipsis_0.3.2
[49] rmarkdown_2.11 httr_1.4.2 rstudioapi_0.13
[52] R6_2.5.1 git2r_0.29.0 compiler_4.1.2