Ingenuity Pathway Analysis
Ha Tran
2024-01-05
Last updated: 2024-08-02
Checks: 7 0
Knit directory: 5_Treg_uNK/1_analysis/
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| Rmd | 73ae14f | Ha Tran | 2024-08-02 | Large update with final visualisations |
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| Rmd | a5cdd4e | git | 2024-03-25 | switching os |
| Rmd | d0ea132 | Ha Manh Tran | 2024-02-15 | windows crashed |
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| Rmd | d8d23ee | tranmanhha135 | 2024-01-13 | im on holiday |
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| Rmd | 221e2fa | tranmanhha135 | 2024-01-10 | fixed error |
| Rmd | 7d64f82 | tranmanhha135 | 2024-01-09 | completed ORA GO |
| Rmd | 05fa0b3 | tranmanhha135 | 2024-01-06 | added description |
Data Setup
# working with data
library(showtext)
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)
library(pheatmap)
library(ComplexHeatmap)
library(DT)
library(extrafont)
library(readxl)
library(patchwork)
# Visualisation:
library(VennDiagram)
library(kableExtra)
library(ggplot2)
library(grid)
library(pander)
library(cowplot)
library(viridis)
library(igraph)
library(ggalluvial)
library(RColorBrewer)
# Custom ggplot
library(ggplotify)
library(ggbiplot)
library(ggrepel)
library(pandoc)
library(knitr)
opts_knit$set(progress = FALSE, verbose = FALSE)
opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE)IPA analysis
Regulated Pathways
Venn diagram
Disease and Function
Venn diagram
Dot plot
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Australia/Adelaide
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] stringi_1.8.4 knitr_1.48 pandoc_0.2.0
[4] ggrepel_0.9.5.9999 ggbiplot_0.6.2 ggplotify_0.1.2
[7] RColorBrewer_1.1-3 ggalluvial_0.12.5 igraph_2.0.3
[10] viridis_0.6.5 viridisLite_0.4.2 cowplot_1.1.3
[13] pander_0.6.5 kableExtra_1.4.0 VennDiagram_1.7.3
[16] futile.logger_1.4.3 patchwork_1.2.0 readxl_1.4.3
[19] extrafont_0.19 DT_0.33 ComplexHeatmap_2.20.0
[22] pheatmap_1.0.12 lubridate_1.9.3 forcats_1.0.0
[25] stringr_1.5.1 purrr_1.0.2 tidyr_1.3.1
[28] ggplot2_3.5.1 tidyverse_2.0.0 reshape2_1.4.4
[31] tibble_3.2.1 readr_2.1.5 magrittr_2.0.3
[34] dplyr_1.1.4 showtext_0.9-7 showtextdb_3.0
[37] sysfonts_0.8.9
loaded via a namespace (and not attached):
[1] gridExtra_2.3 formatR_1.14 rlang_1.1.4
[4] clue_0.3-65 GetoptLong_1.0.5 git2r_0.33.0
[7] matrixStats_1.3.0 compiler_4.4.1 png_0.1-8
[10] systemfonts_1.1.0 vctrs_0.6.5 pkgconfig_2.0.3
[13] shape_1.4.6.1 crayon_1.5.3 fastmap_1.2.0
[16] magick_2.8.4 labeling_0.4.3 utf8_1.2.4
[19] promises_1.3.0 rmarkdown_2.27 tzdb_0.4.0
[22] ragg_1.3.2 xfun_0.46 cachem_1.1.0
[25] jsonlite_1.8.8 highr_0.11 later_1.3.2
[28] parallel_4.4.1 cluster_2.1.6 R6_2.5.1
[31] bslib_0.8.0 extrafontdb_1.0 jquerylib_0.1.4
[34] cellranger_1.1.0 Rcpp_1.0.13 iterators_1.0.14
[37] IRanges_2.38.1 httpuv_1.6.15 timechange_0.3.0
[40] tidyselect_1.2.1 rstudioapi_0.16.0 yaml_2.3.10
[43] doParallel_1.0.17 codetools_0.2-20 plyr_1.8.9
[46] withr_3.0.1 evaluate_0.24.0 gridGraphics_0.5-1
[49] lambda.r_1.2.4 xml2_1.3.6 circlize_0.4.16
[52] pillar_1.9.0 whisker_0.4.1 foreach_1.5.2
[55] stats4_4.4.1 generics_0.1.3 rprojroot_2.0.4
[58] S4Vectors_0.42.1 hms_1.1.3 munsell_0.5.1
[61] scales_1.3.0 glue_1.7.0 tools_4.4.1
[64] fs_1.6.4 Rttf2pt1_1.3.12 colorspace_2.1-1
[67] cli_3.6.3 rappdirs_0.3.3 textshaping_0.4.0
[70] workflowr_1.7.1 futile.options_1.0.1 fansi_1.0.6
[73] svglite_2.1.3 gtable_0.3.5 yulab.utils_0.1.5
[76] sass_0.4.9 digest_0.6.36 BiocGenerics_0.50.0
[79] farver_2.1.2 rjson_0.2.21 htmlwidgets_1.6.4
[82] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
[85] here_1.0.1 GlobalOptions_0.1.2