Analysis of CRC Spatial Transcriptomics data from 10X: Exploring Liana Results
Alberto Valdeolivas Urbelz (PS-Biomics&Path)
03 February, 2023
1 Introduction
library(ggplot2)
library(vctrs)
library(dplyr)
library(patchwork, lib.loc = "/apps/rocs/2020.08/cascadelake/software/R/4.1.2-foss-2020a/lib64/R/library")
library(Seurat)
library(tibble)
library(readr)
library(stringr)
library(cowplot)
library(RColorBrewer)
library(liana)
data_directory <- params$data_directory
analysis_name <- params$analysis_name
input_files <- "IntermediaryFiles/MergeClustering/"
input_names <- "lianaResults.rds"
files_to_read <- paste0(data_directory, analysis_name,input_files,input_names)
results_directory <- paste0(data_directory, analysis_name, input_files)Reading Seurat objects
liana_results <- readRDS(files_to_read)Plotting results for our top ligands.
my_ligands <- c("CXCL14", "LUM", "THBS2", "RNF43","PLAU", "DCN", "MMP1")
liana_significant_myligands <- liana_results %>%
dplyr::filter(ligand %in% my_ligands) %>%
dplyr::filter(source %in% c("1", "0"), target %in% c("0", "1")) %>%
dplyr::filter(aggregate_rank < 0.01) %>%
dplyr::mutate(source = ifelse(source == "1", "TME", "Tumor")) %>%
dplyr::mutate(target = ifelse(target == "1", "TME", "Tumor"))
liana_significant_myligands %>%
# top_n(25, desc(aggregate_rank)) %>%
liana_dotplot(source_groups = c("TME", "Tumor"),
target_groups = c("TME","Tumor"), show_complex = FALSE) +
# target_groups = unique(overlapping_liana_results_sc$target)) +
theme(axis.text.y = element_text(size = 10, colour = "black", face = "bold"),
axis.text.x = element_text(size = 10, colour = "black", face = "bold"),
axis.title.x = element_text(size = 14),
strip.background = element_rect(fill = NA),
strip.text = element_text(size = 12, colour = "black", face ="bold"),
legend.text = element_text(size = 12), legend.title = element_text(size=14)) +
scale_color_gradientn(colours = RColorBrewer::brewer.pal(n=5, name = "Reds")) +
scale_size_continuous(range = c(3, 7))
2 Session Info Details
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Fedora 33 (Container Image)
##
## Matrix products: default
## BLAS/LAPACK: /apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/lib/libopenblas_skylakexp-r0.3.9.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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] liana_0.1.6 RColorBrewer_1.1-3 cowplot_1.1.1
## [4] stringr_1.4.0 readr_2.1.2 tibble_3.1.7
## [7] sp_1.5-0 SeuratObject_4.1.0 Seurat_4.1.0
## [10] patchwork_1.1.1 dplyr_1.0.9 vctrs_0.4.1
## [13] ggplot2_3.3.6 BiocManager_1.30.18
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.2 reticulate_1.25
## [3] tidyselect_1.1.2 htmlwidgets_1.5.4
## [5] grid_4.1.2 BiocParallel_1.28.3
## [7] Rtsne_0.16 munsell_0.5.0
## [9] ScaledMatrix_1.2.0 codetools_0.2-18
## [11] ica_1.0-2 statmod_1.4.36
## [13] scran_1.22.1 future_1.26.1
## [15] miniUI_0.1.1.1 withr_2.5.0
## [17] spatstat.random_2.2-0 colorspace_2.1-0
## [19] progressr_0.10.1 Biobase_2.54.0
## [21] highr_0.9 logger_0.2.2
## [23] knitr_1.39 rstudioapi_0.13
## [25] stats4_4.1.2 SingleCellExperiment_1.16.0
## [27] ROCR_1.0-11 tensor_1.5
## [29] listenv_0.8.0 labeling_0.4.2
## [31] MatrixGenerics_1.6.0 GenomeInfoDbData_1.2.7
## [33] polyclip_1.10-0 farver_2.1.0
## [35] parallelly_1.32.0 generics_0.1.2
## [37] xfun_0.31 R6_2.5.1
## [39] doParallel_1.0.17 GenomeInfoDb_1.30.1
## [41] clue_0.3-61 rsvd_1.0.5
## [43] locfit_1.5-9.5 bitops_1.0-7
## [45] spatstat.utils_2.3-1 DelayedArray_0.20.0
## [47] assertthat_0.2.1 promises_1.2.0.1
## [49] scales_1.2.0 rgeos_0.5-10
## [51] gtable_0.3.0 beachmat_2.10.0
## [53] globals_0.15.0 goftest_1.2-3
## [55] rlang_1.0.2 GlobalOptions_0.1.2
## [57] splines_4.1.2 lazyeval_0.2.2
## [59] spatstat.geom_2.4-0 checkmate_2.1.0
## [61] yaml_2.3.5 reshape2_1.4.4
## [63] abind_1.4-7 backports_1.4.1
## [65] httpuv_1.6.5 tools_4.1.2
## [67] ellipsis_0.3.2 spatstat.core_2.4-4
## [69] jquerylib_0.1.4 BiocGenerics_0.40.0
## [71] ggridges_0.5.3 Rcpp_1.0.8.3
## [73] plyr_1.8.7 sparseMatrixStats_1.6.0
## [75] progress_1.2.2 zlibbioc_1.40.0
## [77] purrr_0.3.4 RCurl_1.98-1.7
## [79] prettyunits_1.1.1 rpart_4.1.16
## [81] deldir_1.0-6 viridis_0.6.2
## [83] pbapply_1.5-0 GetoptLong_1.0.5
## [85] S4Vectors_0.32.4 zoo_1.8-10
## [87] SummarizedExperiment_1.24.0 ggrepel_0.9.1
## [89] cluster_2.1.3 magrittr_2.0.3
## [91] data.table_1.14.2 scattermore_0.8
## [93] circlize_0.4.15 lmtest_0.9-40
## [95] RANN_2.6.1 fitdistrplus_1.1-8
## [97] matrixStats_0.62.0 hms_1.1.1
## [99] mime_0.12 evaluate_0.15
## [101] xtable_1.8-6 readxl_1.4.0
## [103] IRanges_2.28.0 gridExtra_2.3
## [105] shape_1.4.6 compiler_4.1.2
## [107] KernSmooth_2.23-20 crayon_1.5.1
## [109] htmltools_0.5.2 mgcv_1.8-40
## [111] later_1.3.0 tzdb_0.3.0
## [113] tidyr_1.2.0 DBI_1.1.3
## [115] ComplexHeatmap_2.10.0 MASS_7.3-57
## [117] rappdirs_0.3.3 Matrix_1.4-2
## [119] cli_3.3.0 metapod_1.2.0
## [121] parallel_4.1.2 igraph_1.3.2
## [123] GenomicRanges_1.46.1 pkgconfig_2.0.3
## [125] OmnipathR_3.5.6 scuttle_1.4.0
## [127] plotly_4.10.0 spatstat.sparse_2.1-1
## [129] xml2_1.3.3 foreach_1.5.2
## [131] bslib_0.3.1 dqrng_0.3.0
## [133] XVector_0.34.0 rvest_1.0.2
## [135] digest_0.6.29 sctransform_0.3.3
## [137] RcppAnnoy_0.0.19 spatstat.data_2.2-0
## [139] rmarkdown_2.14 cellranger_1.1.0
## [141] leiden_0.4.2 edgeR_3.36.0
## [143] uwot_0.1.11 DelayedMatrixStats_1.16.0
## [145] curl_4.3.2 shiny_1.7.1
## [147] rjson_0.2.21 lifecycle_1.0.1
## [149] nlme_3.1-158 jsonlite_1.8.0
## [151] BiocNeighbors_1.12.0 limma_3.50.3
## [153] viridisLite_0.4.0 fansi_1.0.3
## [155] pillar_1.7.0 lattice_0.20-45
## [157] fastmap_1.1.0 httr_1.4.3
## [159] survival_3.3-1 glue_1.6.2
## [161] png_0.1-7 iterators_1.0.14
## [163] bluster_1.4.0 stringi_1.7.6
## [165] sass_0.4.1 BiocSingular_1.10.0
## [167] irlba_2.3.5 future.apply_1.9.0