Figures & Tables

workflowr

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Last updated: 2023-09-28

Checks: 7 0

Knit directory: cirrhosis-metabolism/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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Repository version: 1eb8773

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/other/
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    Ignored:    figures/CYP.pdf
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    Ignored:    figures/Canalicular.pdf
    Ignored:    figures/Canalicular_hs.pdf
    Ignored:    figures/DH.pdf
    Ignored:    figures/DH_hs.pdf
    Ignored:    figures/EPH.pdf
    Ignored:    figures/EPH_hs.pdf
    Ignored:    figures/FMO.pdf
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    Ignored:    figures/GST.pdf
    Ignored:    figures/GST_hs.pdf
    Ignored:    figures/MAO.pdf
    Ignored:    figures/MAO_hs.pdf
    Ignored:    figures/MT.pdf
    Ignored:    figures/MT_hs.pdf
    Ignored:    figures/NAT.pdf
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    Ignored:    output/mouse-chronic-ccl4/genesets_degs_hs.rds
    Ignored:    output/mouse-chronic-ccl4/metabolic_genes.rds
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    Ignored:    output/seddik/
    Ignored:    renv/library/
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    Ignored:    renv/staging/
    Ignored:    tables/metabolic_carrier_genes.xlsx

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/03_figures_and_tables.Rmd) and HTML (docs/03_figures_and_tables.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	1eb8773	christianholland	2023-09-28	adjusted EPH gene set by only including ephx1-4 genes
Rmd	9887126	christianholland	2023-09-28	updated the supplementary table of metabolic and carrier genes with the results of differential gene expression analysis
Rmd	2e0a61e	christianholland	2023-09-28	updated names of metabolic gene sets
html	d429adc	christianholland	2023-01-08	Build site.
html	4323bde	christianholland	2023-01-08	Build site.
Rmd	08bc4b3	christianholland	2023-01-08	wflow_publish("analysis/*.Rmd")
html	d8910e2	christianholland	2023-01-07	Build site.
html	b620f23	christianholland	2023-01-07	Build site.
Rmd	a086fbd	christianholland	2023-01-07	wflow_publish("analysis/*.Rmd")

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Introduction

This script generates the publication ready figures and supplementary tables

Libraries and sources

These libraries and sources are used for this analysis.

# data wrangling
library(tidyverse)

# plotting
library(patchwork)
library(gtools)

# colors
library(AachenColorPalette)

# display tables
library(DT)

# development helpers
library(here)
library(devtools)

# other
library(openxlsx)

# source scripts
source(here("code/plots.R"))

# source scripts from external projects
base_url <- "https://raw.githubusercontent.com/saezlab/liver-disease-atlas"
source_url(file.path(base_url, "master", "code", "utils-plots.R"))

Figures

Figure 1

PCA

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4323bde	christianholland	2023-01-08

Top DEGs

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4323bde	christianholland	2023-01-08

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Figure 2

Single correlations

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4323bde	christianholland	2023-01-08

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Correlation heatmap

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4323bde	christianholland	2023-01-08

Top DEGs

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4323bde	christianholland	2023-01-08

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Tables

List of metabolic and carrier genes with degs

Joining, by = "gene"
Joining, by = "gene"

Session information

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] openxlsx_4.2.5.1         devtools_2.4.5.9000      usethis_2.1.6           
 [4] here_1.0.1               DT_0.26                  AachenColorPalette_1.1.3
 [7] gtools_3.9.4             patchwork_1.1.2          forcats_0.5.2           
[10] stringr_1.4.1            dplyr_1.0.10             purrr_0.3.5             
[13] readr_2.1.3              tidyr_1.2.1              tibble_3.1.8            
[16] ggplot2_3.3.6            tidyverse_1.3.2          workflowr_1.7.0         

loaded via a namespace (and not attached):
 [1] googledrive_2.0.0   colorspace_2.0-3    ellipsis_0.3.2     
 [4] rprojroot_2.0.3     fs_1.5.2            rstudioapi_0.14    
 [7] farver_2.1.1        remotes_2.4.2       fansi_1.0.3        
[10] lubridate_1.8.0     xml2_1.3.3          splines_4.2.1      
[13] cachem_1.0.6        knitr_1.40          pkgload_1.3.0      
[16] jsonlite_1.8.3      broom_1.0.1         dbplyr_2.2.1       
[19] shiny_1.7.2         compiler_4.2.1      httr_1.4.4         
[22] backports_1.4.1     Matrix_1.4-1        assertthat_0.2.1   
[25] fastmap_1.1.0       gargle_1.2.1        cli_3.4.1          
[28] later_1.3.0         htmltools_0.5.3     prettyunits_1.1.1  
[31] tools_4.2.1         gtable_0.3.1        glue_1.6.2         
[34] Rcpp_1.0.9          cellranger_1.1.0    jquerylib_0.1.4    
[37] vctrs_0.5.0         nlme_3.1-157        crosstalk_1.2.0    
[40] xfun_0.34           ps_1.7.1            rvest_1.0.3        
[43] mime_0.12           miniUI_0.1.1.1      lifecycle_1.0.3    
[46] renv_0.16.0         googlesheets4_1.0.1 getPass_0.2-2      
[49] scales_1.2.1        ragg_1.2.3          hms_1.1.2          
[52] promises_1.2.0.1    yaml_2.3.6          curl_4.3.3         
[55] memoise_2.0.1       sass_0.4.2          stringi_1.7.8      
[58] highr_0.9           pkgbuild_1.3.1      zip_2.2.1          
[61] rlang_1.0.6         pkgconfig_2.0.3     systemfonts_1.0.4  
[64] lattice_0.20-45     evaluate_0.17       htmlwidgets_1.5.4  
[67] labeling_0.4.2      cowplot_1.1.1       processx_3.7.0     
[70] tidyselect_1.2.0    magrittr_2.0.3      R6_2.5.1           
[73] generics_0.1.3      profvis_0.3.7       DBI_1.1.3          
[76] pillar_1.8.1        haven_2.5.1         whisker_0.4        
[79] withr_2.5.0         mgcv_1.8-40         modelr_0.1.9       
[82] crayon_1.5.2        utf8_1.2.2          tzdb_0.3.0         
[85] rmarkdown_2.17      urlchecker_1.0.1    grid_4.2.1         
[88] readxl_1.4.1        callr_3.7.2         git2r_0.30.1       
[91] reprex_2.0.2        digest_0.6.30       xtable_1.8-4       
[94] httpuv_1.6.6        textshaping_0.3.6   munsell_0.5.0      
[97] bslib_0.4.0         sessioninfo_1.2.2