Reactome Analysis
Ha M. Tran
22/08/2021
Last updated: 2023-09-16
Checks: 7 0
Knit directory:
Mouse_endometrial_transcriptome_2023/1_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 18c6463 | Ha Manh Tran | 2023-09-16 | Added KEGG copyright permission and changed kable |
| html | b44640a | Ha Manh Tran | 2023-01-23 | Build site. |
| Rmd | eb10bef | Ha Manh Tran | 2023-01-22 | workflowr::wflow_publish(here::here("1_analysis/*.Rmd")) |
| html | 8c9178d | tranmanhha135 | 2023-01-21 | added png |
| html | d578f46 | Ha Manh Tran | 2023-01-21 | Build site. |
| html | 159f352 | tranmanhha135 | 2023-01-21 | adding for pathview |
| Rmd | 4d51a4e | tranmanhha135 | 2023-01-20 | test png |
| html | 4d51a4e | tranmanhha135 | 2023-01-20 | test png |
| html | 691cf34 | Ha Manh Tran | 2023-01-20 | Build site. |
| Rmd | 7f6bab2 | Ha Manh Tran | 2023-01-20 | workflowr::wflow_publish(here::here("1_analysis/*.Rmd")) |
| Rmd | b6cf190 | tranmanhha135 | 2023-01-19 | quick commit |
| Rmd | 3119fad | tranmanhha135 | 2022-11-05 | build website |
| html | 3119fad | tranmanhha135 | 2022-11-05 | build website |
Data Setup
# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)
# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
library(pander)
library(cowplot)
library(pheatmap)
library(DT)
# Custom ggplot
library(ggbiplot)
library(ggrepel)
theme_set(theme_light())
pub <- readRDS(here::here("0_data/RDS_objects/pub.rds"))
DT <- readRDS(here::here("0_data/RDS_objects/DT.rds"))
# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
library(ReactomePA)Import DGElist Data
DGElist object containing the raw feature count, sample metadata, and gene metadata, created in the Set Up stage.
# load DGElist previously created in the set up
dge <- readRDS(here::here("0_data/RDS_objects/dge.rds"))
fc <- readRDS(here::here("0_data/RDS_objects/fc.rds"))
lfc <- readRDS(here::here("0_data/RDS_objects/lfc.rds"))
lmTreat <- readRDS(here::here("0_data/RDS_objects/lmTreat.rds"))
lmTreat_sig <- readRDS(here::here("0_data/RDS_objects/lmTreat_sig.rds"))Reactome
FC=1.05
p=1Enriched pathways
reactome=list()
reactome_all=list()
reactome_sig=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
reactome[[x]] <- enrichPathway(gene = lmTreat_sig[[x]]$entrezid, organism = "mouse", pvalueCutoff = 0.05, pAdjustMethod = "fdr", readable = T)
reactome_all[[x]] <- reactome[[x]]@result
reactome_sig[[x]] <- reactome_all[[x]] %>% dplyr::filter(p.adjust <= 0.05) %>%
separate(col = BgRatio, sep = "/", into = c("Total", "Universe")) %>%
dplyr::mutate(
logFDR = -log(p.adjust, 10),
GeneRatio = Count / as.numeric(Total))%>%
dplyr::select(c("Description", "GeneRatio", "pvalue", "p.adjust", "logFDR", "qvalue", "geneID", "Count"))
# at the beginnning of a word (after 35 characters), add a newline. shorten the y axis for dot plot
reactome_sig[[x]]$Description <- sub(pattern = "(.{1,55})(?:$| )",
replacement = "\\1\n",
x = reactome_sig[[x]]$Description)
# remove the additional newline at the end of the string
reactome_sig[[x]]$Description <- sub(pattern = "\n$",
replacement = "",
x = reactome_sig[[x]]$Description)
}
reactome_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
DT(.,"Enriched pathways") # kable() %>%
# kable_styling(bootstrap_options = c("striped", "hover")) %>%
# scroll_box(height = "600px")Dot plot
react_dot=list()
upset=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
react_dot[[x]] <- ggplot(reactome_sig[[x]][1:12, ]) +
geom_point(aes(x = GeneRatio, y = reorder(Description, GeneRatio), colour = logFDR, size = Count)) +
scale_color_gradient(low = "dodgerblue3", high = "firebrick3", limits = c(0, NA)) +
scale_size(range = c(1.5,5)) +
ggtitle("Reactome Pathways") +
ylab(label = "") +
xlab(label = "Gene Ratio") +
labs(color = expression("-log"[10] * "FDR"), size = "Gene Counts")
ggsave(filename = paste0("react_dot_", x, ".svg"), plot = react_dot[[x]] + pub, path = here::here("2_plots/reactome/"),
width = 250, height = 130, units = "mm")
upset[[x]] <- upsetplot(x = reactome[[x]], 9)
ggsave(filename = paste0("upset_react_", fc[i], ".svg"), plot = upset[[x]], path = here::here("2_plots/reactome/"))
}
react_dot[[p]]
FC=1.1
p=p+1Enriched pathways
reactome_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
DT(.,"Enriched pathways") # kable() %>%
# kable_styling(bootstrap_options = c("striped", "hover")) %>%
# scroll_box(height = "600px")Dot plot
react_dot[[p]]
FC=1.5
p=p+1Enriched pathways
reactome_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
DT(.,"Enriched pathways") # kable() %>%
# kable_styling(bootstrap_options = c("striped", "hover")) %>%
# scroll_box(height = "600px")Dot plot
react_dot[[p]]
Export Data
# save to csv
writexl::write_xlsx(x = reactome_all, here::here("3_output/reactome_all.xlsx"))
writexl::write_xlsx(x = reactome_sig, here::here("3_output/reactome_sig.xlsx"))
sessionInfo()R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
time zone: Australia/Adelaide
tzcode source: internal
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ReactomePA_1.44.0 enrichplot_1.20.1 org.Mm.eg.db_3.17.0
[4] AnnotationDbi_1.62.2 IRanges_2.34.1 S4Vectors_0.38.1
[7] Biobase_2.60.0 BiocGenerics_0.46.0 clusterProfiler_4.8.3
[10] Glimma_2.10.0 edgeR_3.42.4 limma_3.56.2
[13] ggrepel_0.9.3 ggbiplot_0.55 scales_1.2.1
[16] plyr_1.8.8 DT_0.29 pheatmap_1.0.12
[19] cowplot_1.1.1 pander_0.6.5 kableExtra_1.3.4
[22] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[25] purrr_1.0.1 tidyr_1.3.0 ggplot2_3.4.3
[28] tidyverse_2.0.0 reshape2_1.4.4 tibble_3.2.1
[31] readr_2.1.4 magrittr_2.0.3 dplyr_1.1.2
loaded via a namespace (and not attached):
[1] splines_4.3.1 later_1.3.1
[3] bitops_1.0-7 ggplotify_0.1.2
[5] polyclip_1.10-4 graph_1.78.0
[7] lifecycle_1.0.3 rprojroot_2.0.3
[9] lattice_0.21-8 MASS_7.3-60
[11] crosstalk_1.2.0 sass_0.4.7
[13] rmarkdown_2.24 jquerylib_0.1.4
[15] yaml_2.3.7 httpuv_1.6.11
[17] DBI_1.1.3 RColorBrewer_1.1-3
[19] abind_1.4-5 zlibbioc_1.46.0
[21] rvest_1.0.3 GenomicRanges_1.52.0
[23] ggraph_2.1.0 RCurl_1.98-1.12
[25] yulab.utils_0.0.9 tweenr_2.0.2
[27] rappdirs_0.3.3 git2r_0.32.0
[29] GenomeInfoDbData_1.2.10 tidytree_0.4.5
[31] reactome.db_1.84.0 svglite_2.1.1
[33] codetools_0.2-19 DelayedArray_0.26.7
[35] DOSE_3.26.1 xml2_1.3.5
[37] ggforce_0.4.1 tidyselect_1.2.0
[39] aplot_0.2.1 farver_2.1.1
[41] viridis_0.6.4 matrixStats_1.0.0
[43] webshot_0.5.5 jsonlite_1.8.7
[45] ellipsis_0.3.2 tidygraph_1.2.3
[47] systemfonts_1.0.4 tools_4.3.1
[49] ragg_1.2.5 treeio_1.24.3
[51] Rcpp_1.0.11 glue_1.6.2
[53] gridExtra_2.3 xfun_0.39
[55] here_1.0.1 DESeq2_1.40.2
[57] qvalue_2.32.0 MatrixGenerics_1.12.3
[59] GenomeInfoDb_1.36.3 withr_2.5.0
[61] fastmap_1.1.1 fansi_1.0.4
[63] digest_0.6.33 timechange_0.2.0
[65] R6_2.5.1 gridGraphics_0.5-1
[67] textshaping_0.3.6 colorspace_2.1-0
[69] GO.db_3.17.0 RSQLite_2.3.1
[71] utf8_1.2.3 generics_0.1.3
[73] data.table_1.14.8 graphlayouts_1.0.0
[75] httr_1.4.7 htmlwidgets_1.6.2
[77] S4Arrays_1.0.6 scatterpie_0.2.1
[79] graphite_1.46.0 whisker_0.4.1
[81] pkgconfig_2.0.3 gtable_0.3.4
[83] blob_1.2.4 workflowr_1.7.1
[85] XVector_0.40.0 shadowtext_0.1.2
[87] htmltools_0.5.5 fgsea_1.26.0
[89] ggupset_0.3.0 png_0.1-8
[91] ggfun_0.1.3 knitr_1.44
[93] rstudioapi_0.15.0 tzdb_0.4.0
[95] nlme_3.1-163 cachem_1.0.8
[97] parallel_4.3.1 HDO.db_0.99.1
[99] pillar_1.9.0 vctrs_0.6.3
[101] promises_1.2.0.1 evaluate_0.21
[103] cli_3.6.1 locfit_1.5-9.8
[105] compiler_4.3.1 rlang_1.1.1
[107] crayon_1.5.2 labeling_0.4.3
[109] fs_1.6.3 writexl_1.4.2
[111] stringi_1.7.12 viridisLite_0.4.2
[113] BiocParallel_1.34.2 munsell_0.5.0
[115] Biostrings_2.68.1 lazyeval_0.2.2
[117] GOSemSim_2.26.1 Matrix_1.6-1
[119] hms_1.1.3 patchwork_1.1.3
[121] bit64_4.0.5 KEGGREST_1.40.0
[123] SummarizedExperiment_1.30.2 igraph_1.5.1
[125] memoise_2.0.1 bslib_0.5.1
[127] ggtree_3.8.2 fastmatch_1.1-4
[129] bit_4.0.5 downloader_0.4
[131] ape_5.7-1 gson_0.1.0