Pathway similarities
1 May 2024
Package
pareg 1.8.0
Contents
1 Prelude
library(tidyverse)
library(ComplexHeatmap)
library(circlize)
library(GGally)
library(pareg)
data(pathway_similarities, package = "pareg")
set.seed(42)2 Introduction
Pathway similarities describe how similar two pathways are (you’re welcome). For example, when interpreting pathways as gene sets, one could count how many genes are shared between two sets. Many more sophisticated methods, such as the Jaccard index, exist (Gu and Huebschmann 2021).
pareg provides various pre-computed similarity measures (jaccard, overlap_coefficient, semantic) for selected pathway databases (C2@CP:KEGG, C5@GO:BP) in matrix form.
mat <- pathway_similarities$`C2@CP:KEGG`$jaccard %>%
as_dense_sim()
mat[1:3, 1:3]## hsa00970 hsa05340 hsa04621
## hsa00970 1 0.000000000 0.000000000
## hsa05340 0 1.000000000 0.008196721
## hsa04621 0 0.008196721 1.000000000Heatmap(
mat,
name = "similarity",
col = colorRamp2(c(0, 1), c("white", "black")),
show_row_names = FALSE,
show_column_names = FALSE
)
3 Comparison of similarity measures
On the Gene Ontology’s Biological Process subcategory, we can observe how much pathway similarity measures can differ from each other.
df_sim <- pathway_similarities$`C5@GO:BP` %>%
map_dfr(function(mat) {
if (is.null(mat)) {
return(NULL)
}
mat %>%
as_dense_sim() %>%
as.data.frame %>%
rownames_to_column() %>%
pivot_longer(-rowname)
}, .id = "measure") %>%
filter(value > 0) %>%
pivot_wider(names_from = measure, values_from = value) %>%
select(-rowname, -name)
ggpairs(df_sim) +
theme_minimal()## Warning: Removed 514552 rows containing non-finite outside the scale range
## (`stat_density()`).## Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
## Removed 514552 rows containing missing values## Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
## Removed 586334 rows containing missing values## Warning: Removed 514552 rows containing missing values or values outside the scale range
## (`geom_point()`).## Warning: Removed 514552 rows containing non-finite outside the scale range
## (`stat_density()`).## Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
## Removed 586334 rows containing missing values## Warning: Removed 586334 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Removed 586334 rows containing missing values or values outside the scale range
## (`geom_point()`).## Warning: Removed 71782 rows containing non-finite outside the scale range
## (`stat_density()`).
4 Session information
sessionInfo()## R version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /var/cache/basilisk/1.16.0/pareg/1.8.0/pareg/lib/libmkl_rt.so.1; LAPACK version 3.9.0
##
## 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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] GGally_2.2.1 circlize_0.4.16 pareg_1.8.0
## [4] tfprobability_0.15.1 tensorflow_2.16.0 enrichplot_1.24.0
## [7] ComplexHeatmap_2.20.0 lubridate_1.9.3 forcats_1.0.0
## [10] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
## [13] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
## [16] tidyverse_2.0.0 ggraph_2.2.1 ggplot2_3.5.1
## [19] BiocStyle_2.32.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.4.0 later_1.3.2 ggplotify_0.1.2
## [4] filelock_1.0.3 polyclip_1.10-6 basilisk.utils_1.16.0
## [7] lifecycle_1.0.4 doParallel_1.0.17 globals_0.16.3
## [10] lattice_0.22-6 MASS_7.3-60.2 magrittr_2.0.3
## [13] sass_0.4.9 rmarkdown_2.26 jquerylib_0.1.4
## [16] yaml_2.3.8 remotes_2.5.0 httpuv_1.6.15
## [19] doRNG_1.8.6 sessioninfo_1.2.2 pkgbuild_1.4.4
## [22] reticulate_1.36.1 cowplot_1.1.3 DBI_1.2.2
## [25] RColorBrewer_1.1-3 keras_2.15.0 pkgload_1.3.4
## [28] zlibbioc_1.50.0 BiocGenerics_0.50.0 yulab.utils_0.1.4
## [31] tweenr_2.0.3 GenomeInfoDbData_1.2.12 IRanges_2.38.0
## [34] S4Vectors_0.42.0 ggrepel_0.9.5 listenv_0.9.1
## [37] tidytree_0.4.6 parallelly_1.37.1 codetools_0.2-20
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## [58] ggnewscale_0.4.10 progress_1.2.3 tools_4.4.0
## [61] treeio_1.28.0 Rcpp_1.0.12 glue_1.7.0
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## [67] qvalue_2.36.0 usethis_2.2.3 GenomeInfoDb_1.40.0
## [70] withr_3.0.0 BiocManager_1.30.22 fastmap_1.1.1
## [73] basilisk_1.16.0 fansi_1.0.6 digest_0.6.35
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## [94] pkgconfig_2.0.3 gtable_0.3.5 blob_1.2.4
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## [106] png_0.1-8 ggfun_0.1.4 knitr_1.46
## [109] tzdb_0.4.0 reshape2_1.4.4 rjson_0.2.21
## [112] nloptr_2.0.3 nlme_3.1-164 proxy_0.4-27
## [115] cachem_1.0.8 GlobalOptions_0.1.2 parallel_4.4.0
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## [127] cluster_2.1.6 evaluate_0.23 magick_2.8.3
## [130] tinytex_0.50 zeallot_0.1.0 cli_3.6.2
## [133] compiler_4.4.0 rngtools_1.5.2 rlang_1.1.3
## [136] crayon_1.5.2 future.apply_1.11.2 labeling_0.4.3
## [139] plyr_1.8.9 fs_1.6.4 stringi_1.8.3
## [142] viridisLite_0.4.2 BiocParallel_1.38.0 munsell_0.5.1
## [145] Biostrings_2.72.0 lazyeval_0.2.2 devtools_2.4.5
## [148] GOSemSim_2.30.0 Matrix_1.7-0 dir.expiry_1.12.0
## [151] hms_1.1.3 patchwork_1.2.0 bit64_4.0.5
## [154] future_1.33.2 KEGGREST_1.44.0 shiny_1.8.1.1
## [157] highr_0.10 igraph_2.0.3 memoise_2.0.1
## [160] bslib_0.7.0 ggtree_3.12.0 fastmatch_1.1-4
## [163] bit_4.0.5 ape_5.8References
Gu, Zuguang, and Daniel Huebschmann. 2021. “SimplifyEnrichment: An R/Bioconductor Package for Clustering and Visualizing Functional Enrichment Results.” bioRxiv.