13_TCF7_PD1
2021-02-01
Last updated: 2021-02-18
Checks: 6 1
Knit directory: melanoma_publication_old_data/
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Introduction
Preparations
knitr::opts_chunk$set(echo = TRUE, message= FALSE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())Load libraries
First, we will load the libraries needed for this part of the analysis.
sapply(list.files("code/helper_functions", full.names = TRUE), source) code/helper_functions/calculateSummary.R
value ?
visible FALSE
code/helper_functions/censor_dat.R
value ?
visible FALSE
code/helper_functions/detect_mRNA_expression.R
value ?
visible FALSE
code/helper_functions/DistanceToClusterCenter.R
value ?
visible FALSE
code/helper_functions/findMilieu.R code/helper_functions/findPatch.R
value ? ?
visible FALSE FALSE
code/helper_functions/getInfoFromString.R
value ?
visible FALSE
code/helper_functions/getSpotnumber.R
value ?
visible FALSE
code/helper_functions/plotCellCounts.R
value ?
visible FALSE
code/helper_functions/plotCellFractions.R
value ?
visible FALSE
code/helper_functions/plotDist.R
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visible FALSE
code/helper_functions/scatter_function.R
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visible FALSE
code/helper_functions/sceChecks.R
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visible FALSE
code/helper_functions/validityChecks.R
value ?
visible FALSE library(dplyr)
library(SingleCellExperiment)
library(ggplot2)
library(ggridges)Read the data
sce_prot = readRDS(file = "data/data_for_analysis/sce_protein.rds")TCF7 CD8 cells
y <- c(rep(1:10,16),rep(11,7))
# add the group information to the sce object
sce_prot$groups <- y[colData(sce_prot)$ImageNumber]
# now we use the function written by Nils
plotDist(sce_prot["TCF7", sce_prot$celltype == "CD8+ T cell"], plot_type = "ridges",
colour_by = "groups", split_by = "rows",
exprs_values = "asinh") +
geom_vline(xintercept = 1.5)
# define positive cells
sce_prot$TCF7 <- ifelse(assay(sce_prot["TCF7",], "asinh") > 1.5, "TCF7+", "TCF7-")PD1 CD8 cells
y <- c(rep(1:10,16),rep(11,7))
# add the group information to the sce object
sce_prot$groups <- y[colData(sce_prot)$ImageNumber]
# now we use the function written by Nils
plotDist(sce_prot["PD1", sce_prot$celltype == "CD8+ T cell"], plot_type = "ridges",
colour_by = "groups", split_by = "rows",
exprs_values = "asinh") +
geom_vline(xintercept = 1.5)
# define positive cells
sce_prot$PD1 <- ifelse(assay(sce_prot["PD1",], "asinh") > 1.5, "PD1+", "PD1-")Save SCE object
saveRDS(sce_prot, file = "data/data_for_analysis/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] ggridges_0.5.3 ggplot2_3.3.3
[3] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[5] Biobase_2.50.0 GenomicRanges_1.42.0
[7] GenomeInfoDb_1.26.2 IRanges_2.24.1
[9] S4Vectors_0.28.1 BiocGenerics_0.36.0
[11] MatrixGenerics_1.2.0 matrixStats_0.57.0
[13] dplyr_1.0.2 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.20 reshape2_1.4.4
[4] purrr_0.3.4 lattice_0.20-41 colorspace_2.0-0
[7] vctrs_0.3.6 generics_0.1.0 htmltools_0.5.0
[10] yaml_2.2.1 rlang_0.4.10 later_1.1.0.1
[13] pillar_1.4.7 withr_2.3.0 glue_1.4.2
[16] plyr_1.8.6 GenomeInfoDbData_1.2.4 lifecycle_0.2.0
[19] stringr_1.4.0 zlibbioc_1.36.0 munsell_0.5.0
[22] gtable_0.3.0 evaluate_0.14 labeling_0.4.2
[25] knitr_1.30 httpuv_1.5.4 Rcpp_1.0.5
[28] promises_1.1.1 scales_1.1.1 DelayedArray_0.16.0
[31] XVector_0.30.0 farver_2.0.3 fs_1.5.0
[34] digest_0.6.27 stringi_1.5.3 rprojroot_2.0.2
[37] grid_4.0.3 tools_4.0.3 bitops_1.0-6
[40] magrittr_2.0.1 RCurl_1.98-1.2 tibble_3.0.4
[43] crayon_1.3.4 whisker_0.4 pkgconfig_2.0.3
[46] ellipsis_0.3.1 Matrix_1.3-2 rmarkdown_2.6
[49] rstudioapi_0.13 R6_2.5.0 git2r_0.28.0
[52] compiler_4.0.3