Last updated: 2022-02-22
Checks: 7 0
Knit directory: MelanomaIMC/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 73aa800 | toobiwankenobi | 2022-02-22 | add .html for static website |
| Rmd | 64e5fde | toobiwankenobi | 2022-02-16 | change order and naming of supp fig files |
| Rmd | a2860df | toobiwankenobi | 2022-02-09 | adapt code |
| Rmd | b20b6fb | toobiwankenobi | 2022-02-02 | update code for Supp Figures |
| Rmd | 3da15db | toobiwankenobi | 2021-11-24 | changes for revision |
This script generates plots for Supplementary Figure 12.
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 code/helper_functions/read_Data.R
value ? ?
visible FALSE FALSE
code/helper_functions/scatter_function.R
value ?
visible FALSE
code/helper_functions/sceChecks.R
value ?
visible FALSE
code/helper_functions/validityChecks.R
value ?
visible FALSE library(SingleCellExperiment)
library(sf)
library(concaveman)
library(RANN)
library(dplyr)
library(data.table)
library(ggplot2)
library(ggrastr)## Read the data
sce_prot = readRDS(file = "data/data_for_analysis/sce_protein.rds")
sce_prot <- sce_prot[,sce_prot$Location != "CTRL"]example <- findPatch(sce_prot[,sce_prot$Description == "G3"], sce_prot[,colData(sce_prot)$celltype %in% c("B cell", "BnT cell")]$cellID,
'cellID',
'Center_X', 'Center_Y',
'Description',
distance = 15,
min_clust_size = 20,
output_colname = "example_patch")Time difference of 0.4335275 secs
[1] "patches successfully added to sce object"example <- findMilieu(example,
'cellID',
'Center_X', 'Center_Y',
'Description',
'example_patch',
distance = 30,
output_colname = "example_milieu",
plot = TRUE)
| Version | Author | Date |
|---|---|---|
| 235386f | toobiwankenobi | 2022-02-22 |
Time difference of 0.5727913 secs
[1] "milieus successfully added to sce object"example <- findPatch(sce_prot[,sce_prot$Description == "F5"], sce_prot[,colData(sce_prot)$celltype %in% c("B cell", "BnT cell")]$cellID,
'cellID',
'Center_X', 'Center_Y',
'Description',
distance = 15,
min_clust_size = 20,
output_colname = "example_patch")Time difference of 0.4490788 secs
[1] "patches successfully added to sce object"example <- findMilieu(example,
'cellID',
'Center_X', 'Center_Y',
'Description',
'example_patch',
distance = 30,
output_colname = "example_milieu",
plot = TRUE)
| Version | Author | Date |
|---|---|---|
| 235386f | toobiwankenobi | 2022-02-22 |
Time difference of 2.110536 secs
[1] "milieus successfully added to sce object"example <- findPatch(sce_prot[,sce_prot$Description == "B6"], sce_prot[,colData(sce_prot)$celltype %in% c("B cell", "BnT cell")]$cellID,
'cellID',
'Center_X', 'Center_Y',
'Description',
distance = 15,
min_clust_size = 20,
output_colname = "example_patch")Time difference of 1.270536 secs
[1] "patches successfully added to sce object"example <- findMilieu(example,
'cellID',
'Center_X', 'Center_Y',
'Description',
'example_patch',
distance = 30,
output_colname = "example_milieu",
plot = TRUE)
| Version | Author | Date |
|---|---|---|
| 235386f | toobiwankenobi | 2022-02-22 |
Time difference of 1.051517 secs
[1] "milieus successfully added to sce object"
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 ggplot2_3.3.5
[3] data.table_1.14.2 RANN_2.6.1
[5] concaveman_1.1.0 sf_1.0-5
[7] SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[9] Biobase_2.54.0 GenomicRanges_1.46.1
[11] GenomeInfoDb_1.30.1 IRanges_2.28.0
[13] S4Vectors_0.32.3 BiocGenerics_0.40.0
[15] MatrixGenerics_1.6.0 matrixStats_0.61.0
[17] dplyr_1.0.7 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] httr_1.4.2 sass_0.4.0 jsonlite_1.7.3
[4] bslib_0.3.1 assertthat_0.2.1 getPass_0.2-2
[7] highr_0.9 vipor_0.4.5 GenomeInfoDbData_1.2.7
[10] yaml_2.2.2 pillar_1.7.0 lattice_0.20-45
[13] glue_1.6.1 digest_0.6.29 promises_1.2.0.1
[16] XVector_0.34.0 colorspace_2.0-2 htmltools_0.5.2
[19] httpuv_1.6.5 Matrix_1.4-0 pkgconfig_2.0.3
[22] zlibbioc_1.40.0 purrr_0.3.4 scales_1.1.1
[25] processx_3.5.2 whisker_0.4 later_1.3.0
[28] git2r_0.29.0 tibble_3.1.6 proxy_0.4-26
[31] farver_2.1.0 generics_0.1.2 ellipsis_0.3.2
[34] withr_2.4.3 cli_3.1.1 magrittr_2.0.2
[37] crayon_1.4.2 evaluate_0.14 ps_1.6.0
[40] fs_1.5.2 fansi_1.0.2 class_7.3-20
[43] beeswarm_0.4.0 tools_4.1.2 lifecycle_1.0.1
[46] stringr_1.4.0 V8_4.0.0 munsell_0.5.0
[49] DelayedArray_0.20.0 callr_3.7.0 compiler_4.1.2
[52] jquerylib_0.1.4 e1071_1.7-9 rlang_1.0.0
[55] classInt_0.4-3 units_0.7-2 grid_4.1.2
[58] RCurl_1.98-1.5 rstudioapi_0.13 bitops_1.0-7
[61] rmarkdown_2.11 gtable_0.3.0 curl_4.3.2
[64] DBI_1.1.2 R6_2.5.1 knitr_1.37
[67] fastmap_1.1.0 utf8_1.2.2 rprojroot_2.0.2
[70] KernSmooth_2.23-20 ggbeeswarm_0.6.0 stringi_1.7.6
[73] Rcpp_1.0.8 vctrs_0.3.8 tidyselect_1.1.1
[76] xfun_0.29