Last updated: 2022-02-22
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Knit directory: MelanomaIMC/
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This script generates plots for Supplementary Figure 10.
library(SingleCellExperiment)Loading required package: SummarizedExperimentLoading required package: MatrixGenericsLoading required package: matrixStats
Attaching package: 'MatrixGenerics'The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVarsLoading required package: GenomicRangesLoading required package: stats4Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.minLoading required package: S4Vectors
Attaching package: 'S4Vectors'The following objects are masked from 'package:base':
expand.grid, I, unnameLoading required package: IRangesLoading required package: GenomeInfoDbLoading required package: BiobaseWelcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'The following object is masked from 'package:MatrixGenerics':
rowMediansThe following objects are masked from 'package:matrixStats':
anyMissing, rowMedianslibrary(ggplot2)
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──✓ tibble 3.1.6 ✓ dplyr 1.0.7
✓ tidyr 1.2.0 ✓ stringr 1.4.0
✓ readr 2.1.2 ✓ forcats 0.5.1
✓ purrr 0.3.4 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::collapse() masks IRanges::collapse()
x dplyr::combine() masks Biobase::combine(), BiocGenerics::combine()
x dplyr::count() masks matrixStats::count()
x dplyr::desc() masks IRanges::desc()
x tidyr::expand() masks S4Vectors::expand()
x dplyr::filter() masks stats::filter()
x dplyr::first() masks S4Vectors::first()
x dplyr::lag() masks stats::lag()
x ggplot2::Position() masks BiocGenerics::Position(), base::Position()
x purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce()
x dplyr::rename() masks S4Vectors::rename()
x dplyr::slice() masks IRanges::slice()library(dplyr)
library(ggrastr)sce_prot <- readRDS("data/data_for_analysis/sce_protein.rds")
sce_prot <- sce_prot[,sce_prot$Location != "CTRL"]
sce_rna <- readRDS("data/data_for_analysis/sce_RNA.rds")
sce_rna <- sce_rna[,sce_rna$Location != "CTRL"]prot <- as.data.frame(colData(sce_prot)[,c("Center_X", "Center_Y", "Description", "celltype")])
rna <- as.data.frame(colData(sce_rna)[,c("Center_X", "Center_Y", "Description", "celltype")])
prot$dataSet <- "Protein only"
rna$dataSet <- "RNA&Protein"
full <- rbind(prot,rna)
full <- full %>%
mutate(celltype = ifelse(celltype %in% c("B cell", "HLA-DR"), "B cell", "Other"))
# show 10 images with the most B cells
max <- full %>%
filter(dataSet == "Protein only" & celltype == "B cell") %>%
group_by(Description) %>%
summarise(n=n()) %>%
slice_max(n, n=10)
full_sub <- full[full$Description %in% max$Description,]
ggplot(full_sub, aes(x=Center_X, y=Center_Y)) +
geom_point_rast(col=ifelse(full_sub$celltype == "B cell", "springgreen3", "grey"), size=.3,
alpha=ifelse(full_sub$celltype == "B cell", 0.5, 0.1)) +
facet_wrap(~Description+dataSet, ncol = 4, scales = "free") +
theme_bw() +
theme(text = element_text(size=9)) +
xlab("X Coordinate") +
ylab("Y Coordinate")total_hladr <- ncol(sce_rna[,sce_rna$celltype == "HLA-DR"])
sub_hladr <- ncol(sce_rna[,sce_rna$celltype == "HLA-DR" &
sce_rna$Description %in% unique(max$Description)])
percentage <- sub_hladr / total_hladr * 100
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] ggrastr_1.0.1 forcats_0.5.1
[3] stringr_1.4.0 dplyr_1.0.7
[5] purrr_0.3.4 readr_2.1.2
[7] tidyr_1.2.0 tibble_3.1.6
[9] tidyverse_1.3.1 ggplot2_3.3.5
[11] SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[13] Biobase_2.54.0 GenomicRanges_1.46.1
[15] GenomeInfoDb_1.30.1 IRanges_2.28.0
[17] S4Vectors_0.32.3 BiocGenerics_0.40.0
[19] MatrixGenerics_1.6.0 matrixStats_0.61.0
[21] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.5.2 lubridate_1.8.0
[4] httr_1.4.2 rprojroot_2.0.2 tools_4.1.2
[7] backports_1.4.1 bslib_0.3.1 utf8_1.2.2
[10] R6_2.5.1 vipor_0.4.5 DBI_1.1.2
[13] colorspace_2.0-2 withr_2.4.3 tidyselect_1.1.1
[16] processx_3.5.2 compiler_4.1.2 git2r_0.29.0
[19] cli_3.1.1 rvest_1.0.2 Cairo_1.5-14
[22] xml2_1.3.3 DelayedArray_0.20.0 labeling_0.4.2
[25] sass_0.4.0 scales_1.1.1 callr_3.7.0
[28] digest_0.6.29 rmarkdown_2.11 XVector_0.34.0
[31] pkgconfig_2.0.3 htmltools_0.5.2 highr_0.9
[34] dbplyr_2.1.1 fastmap_1.1.0 rlang_1.0.0
[37] readxl_1.3.1 rstudioapi_0.13 farver_2.1.0
[40] jquerylib_0.1.4 generics_0.1.2 jsonlite_1.7.3
[43] RCurl_1.98-1.5 magrittr_2.0.2 GenomeInfoDbData_1.2.7
[46] Matrix_1.4-0 ggbeeswarm_0.6.0 Rcpp_1.0.8
[49] munsell_0.5.0 fansi_1.0.2 lifecycle_1.0.1
[52] stringi_1.7.6 whisker_0.4 yaml_2.2.2
[55] zlibbioc_1.40.0 grid_4.1.2 promises_1.2.0.1
[58] crayon_1.4.2 lattice_0.20-45 haven_2.4.3
[61] hms_1.1.1 knitr_1.37 ps_1.6.0
[64] pillar_1.7.0 reprex_2.0.1 glue_1.6.1
[67] evaluate_0.14 getPass_0.2-2 modelr_0.1.8
[70] vctrs_0.3.8 tzdb_0.2.0 httpuv_1.6.5
[73] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[76] xfun_0.29 broom_0.7.12 later_1.3.0
[79] beeswarm_0.4.0 ellipsis_0.3.2