Last updated: 2023-07-30

Checks: 7 0

Knit directory: Cardiotoxicity/

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.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20230109)

The command set.seed(20230109) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 2c9b724

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 2c9b724. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .RData
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/41588_2018_171_MOESM3_ESMeQTL_ST2_for paper.csv
    Ignored:    data/Arr_GWAS.txt
    Ignored:    data/Arr_geneset.RDS
    Ignored:    data/BC_cell_lines.csv
    Ignored:    data/BurridgeDOXTOX.RDS
    Ignored:    data/CADGWASgene_table.csv
    Ignored:    data/CAD_geneset.RDS
    Ignored:    data/CALIMA_Data/
    Ignored:    data/Clamp_Summary.csv
    Ignored:    data/Cormotif_24_k1-5_raw.RDS
    Ignored:    data/DAgostres24.RDS
    Ignored:    data/DAtable1.csv
    Ignored:    data/DDEMresp_list.csv
    Ignored:    data/DDE_reQTL.txt
    Ignored:    data/DDEresp_list.csv
    Ignored:    data/DEG-GO/
    Ignored:    data/DEG_cormotif.RDS
    Ignored:    data/DF_Plate_Peak.csv
    Ignored:    data/DRC48hoursdata.csv
    Ignored:    data/Da24counts.txt
    Ignored:    data/Dx24counts.txt
    Ignored:    data/Dx_reQTL_specific.txt
    Ignored:    data/Ep24counts.txt
    Ignored:    data/Full_LD_rep.csv
    Ignored:    data/GOIsig.csv
    Ignored:    data/GOplots.R
    Ignored:    data/GTEX_setsimple.csv
    Ignored:    data/GTEX_sig24.RDS
    Ignored:    data/GTEx_gene_list.csv
    Ignored:    data/HFGWASgene_table.csv
    Ignored:    data/HF_geneset.RDS
    Ignored:    data/Heart_Left_Ventricle.v8.egenes.txt
    Ignored:    data/Heatmap_mat.RDS
    Ignored:    data/Heatmap_sig.RDS
    Ignored:    data/Hf_GWAS.txt
    Ignored:    data/K_cluster
    Ignored:    data/K_cluster_kisthree.csv
    Ignored:    data/K_cluster_kistwo.csv
    Ignored:    data/LD50_05via.csv
    Ignored:    data/LDH48hoursdata.csv
    Ignored:    data/Mt24counts.txt
    Ignored:    data/NoRespDEG_final.csv
    Ignored:    data/RINsamplelist.txt
    Ignored:    data/Seonane2019supp1.txt
    Ignored:    data/TMMnormed_x.RDS
    Ignored:    data/TOP2Bi-24hoursGO_analysis.csv
    Ignored:    data/TR24counts.txt
    Ignored:    data/Top2biresp_cluster24h.csv
    Ignored:    data/Var_test_list.RDS
    Ignored:    data/Var_test_list24.RDS
    Ignored:    data/Var_test_list24alt.RDS
    Ignored:    data/Var_test_list3.RDS
    Ignored:    data/Viabilitylistfull.csv
    Ignored:    data/allexpressedgenes.txt
    Ignored:    data/allfinal3hour.RDS
    Ignored:    data/allgenes.txt
    Ignored:    data/allmatrix.RDS
    Ignored:    data/allmymatrix.RDS
    Ignored:    data/annotation_data_frame.RDS
    Ignored:    data/averageviabilitytable.RDS
    Ignored:    data/avgLD50.RDS
    Ignored:    data/avg_LD50.RDS
    Ignored:    data/backGL.txt
    Ignored:    data/burr_genes.RDS
    Ignored:    data/calcium_data.RDS
    Ignored:    data/clamp_summary.RDS
    Ignored:    data/cormotif_3hk1-8.RDS
    Ignored:    data/cormotif_initalK5.RDS
    Ignored:    data/cormotif_initialK5.RDS
    Ignored:    data/cormotif_initialall.RDS
    Ignored:    data/counts24hours.RDS
    Ignored:    data/cpmcount.RDS
    Ignored:    data/cpmnorm_counts.csv
    Ignored:    data/crispr_genes.csv
    Ignored:    data/ctnnt_results.txt
    Ignored:    data/cvd_GWAS.txt
    Ignored:    data/dat_cpm.RDS
    Ignored:    data/data_outline.txt
    Ignored:    data/drug_noveh1.csv
    Ignored:    data/efit2.RDS
    Ignored:    data/efit2_final.RDS
    Ignored:    data/efit2results.RDS
    Ignored:    data/ensembl_backup.RDS
    Ignored:    data/ensgtotal.txt
    Ignored:    data/filcpm_counts.RDS
    Ignored:    data/filenameonly.txt
    Ignored:    data/filtered_cpm_counts.csv
    Ignored:    data/filtered_raw_counts.csv
    Ignored:    data/filtermatrix_x.RDS
    Ignored:    data/folder_05top/
    Ignored:    data/geneDoxonlyQTL.csv
    Ignored:    data/gene_corr_df.RDS
    Ignored:    data/gene_corr_frame.RDS
    Ignored:    data/gene_prob_tran3h.RDS
    Ignored:    data/gene_probabilityk5.RDS
    Ignored:    data/geneset_24.RDS
    Ignored:    data/gostresTop2bi_ER.RDS
    Ignored:    data/gostresTop2bi_LR
    Ignored:    data/gostresTop2bi_LR.RDS
    Ignored:    data/gostresTop2bi_TI.RDS
    Ignored:    data/gostrescoNR
    Ignored:    data/gtex/
    Ignored:    data/heartgenes.csv
    Ignored:    data/hsa_kegg_anno.RDS
    Ignored:    data/individualDRCfile.RDS
    Ignored:    data/individual_DRC48.RDS
    Ignored:    data/individual_LDH48.RDS
    Ignored:    data/indv_noveh1.csv
    Ignored:    data/kegglistDEG.RDS
    Ignored:    data/kegglistDEG24.RDS
    Ignored:    data/kegglistDEG3.RDS
    Ignored:    data/knowfig4.csv
    Ignored:    data/knowfig5.csv
    Ignored:    data/label_list.RDS
    Ignored:    data/ld50_table.csv
    Ignored:    data/mean_vardrug1.csv
    Ignored:    data/mean_varframe.csv
    Ignored:    data/mymatrix.RDS
    Ignored:    data/new_ld50avg.RDS
    Ignored:    data/nonresponse_cluster24h.csv
    Ignored:    data/norm_LDH.csv
    Ignored:    data/norm_counts.csv
    Ignored:    data/old_sets/
    Ignored:    data/organized_drugframe.csv
    Ignored:    data/plan2plot.png
    Ignored:    data/plot_intv_list.RDS
    Ignored:    data/plot_list_DRC.RDS
    Ignored:    data/qvalueEPItemp.RDS
    Ignored:    data/raw_counts.csv
    Ignored:    data/response_cluster24h.csv
    Ignored:    data/sigVDA24.txt
    Ignored:    data/sigVDA3.txt
    Ignored:    data/sigVDX24.txt
    Ignored:    data/sigVDX3.txt
    Ignored:    data/sigVEP24.txt
    Ignored:    data/sigVEP3.txt
    Ignored:    data/sigVMT24.txt
    Ignored:    data/sigVMT3.txt
    Ignored:    data/sigVTR24.txt
    Ignored:    data/sigVTR3.txt
    Ignored:    data/siglist.RDS
    Ignored:    data/siglist_final.RDS
    Ignored:    data/siglist_old.RDS
    Ignored:    data/slope_table.csv
    Ignored:    data/supp_normLDH48.RDS
    Ignored:    data/supp_pca_all_anno.RDS
    Ignored:    data/table3a.omar
    Ignored:    data/testlist.txt
    Ignored:    data/toplistall.RDS
    Ignored:    data/trtonly_24h_genes.RDS
    Ignored:    data/trtonly_3h_genes.RDS
    Ignored:    data/tvl24hour.txt
    Ignored:    data/tvl24hourw.txt
    Ignored:    data/venn_code.R
    Ignored:    data/viability.RDS

Untracked files:
    Untracked:  .RDataTmp
    Untracked:  .RDataTmp1
    Untracked:  .RDataTmp2
    Untracked:  Doxorubicin_vehicle_3_24.csv
    Untracked:  Doxtoplist.csv
    Untracked:  GWAS_list_of_interest.xlsx
    Untracked:  KEGGpathwaylist.R
    Untracked:  OmicNavigator_learn.R
    Untracked:  SigDoxtoplist.csv
    Untracked:  analysis/DRC_analysist.Rmd
    Untracked:  analysis/ciFIT.R
    Untracked:  analysis/enricher.Rmd
    Untracked:  analysis/export_to_excel.R
    Untracked:  analysis/untitled1.R
    Untracked:  code/DRC_plotfigure1.png
    Untracked:  code/constantcode.R
    Untracked:  code/cpm_boxplot.R
    Untracked:  code/extracting_ggplot_data.R
    Untracked:  code/fig1plot.png
    Untracked:  code/figurelegeddrc.png
    Untracked:  code/movingfilesto_ppl.R
    Untracked:  code/pearson_extract_func.R
    Untracked:  code/pearson_tox_extract.R
    Untracked:  code/plot1C.fun.R
    Untracked:  code/spearman_extract_func.R
    Untracked:  code/venndiagramcolor_control.R
    Untracked:  cormotif_probability_genelist.csv
    Untracked:  individual-legenddark2.png
    Untracked:  installed_old.rda
    Untracked:  motif_ER.txt
    Untracked:  motif_LR.txt
    Untracked:  motif_NR.txt
    Untracked:  motif_TI.txt
    Untracked:  output/DNRvenn.RDS
    Untracked:  output/DOXvenn.RDS
    Untracked:  output/EPIvenn.RDS
    Untracked:  output/Figures/
    Untracked:  output/MTXvenn.RDS
    Untracked:  output/Volcanoplot_10
    Untracked:  output/Volcanoplot_10.RDS
    Untracked:  output/allfinal_sup10.RDS
    Untracked:  output/gene_corr_fig9.RDS
    Untracked:  output/legend_b.RDS
    Untracked:  output/motif_ERrep.RDS
    Untracked:  output/motif_LRrep.RDS
    Untracked:  output/motif_NRrep.RDS
    Untracked:  output/motif_TI_rep.RDS
    Untracked:  output/output-old/
    Untracked:  output/rank24genes.csv
    Untracked:  output/rank3genes.csv
    Untracked:  output/supplementary_motif_list_GO.RDS
    Untracked:  output/toptablebydrug.RDS
    Untracked:  output/x_counts.RDS
    Untracked:  reneebasecode.R

Unstaged changes:
    Modified:   output/TNNI_LDH_RNAnormlist.txt
    Modified:   output/daplot.RDS
    Modified:   output/dxplot.RDS
    Modified:   output/epplot.RDS
    Modified:   output/mtplot.RDS
    Modified:   output/plan2plot.png
    Modified:   output/toplistall.csv
    Modified:   output/trplot.RDS
    Modified:   output/veplot.RDS

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.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Figure5.Rmd) and HTML (docs/Figure5.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 2c9b724 reneeisnowhere 2023-07-30 test
html 4bb0b80 reneeisnowhere 2023-07-28 Build site.
Rmd 974fcde reneeisnowhere 2023-07-28 new figures update
html c40aced reneeisnowhere 2023-07-26 Build site.
Rmd 58c7965 reneeisnowhere 2023-07-26 updating figures
html ed18a48 reneeisnowhere 2023-07-07 Build site.
Rmd 63d054a reneeisnowhere 2023-07-07 Various changes to graphs. pending Monday-renames
html 0e3d22d reneeisnowhere 2023-07-06 Build site.
Rmd 6a6c9af reneeisnowhere 2023-07-06 adding fig 5 and changing fig9 heatmap
Rmd a95c83e reneeisnowhere 2023-07-06 update code
html 8f66a2d reneeisnowhere 2023-06-29 Build site.
Rmd 060305d reneeisnowhere 2023-06-29 update in data
html f77112b reneeisnowhere 2023-06-27 Build site.
Rmd ceea93e reneeisnowhere 2023-06-27 adding fig 5 
<environment: R_GlobalEnv>
<environment: R_GlobalEnv>

Figure 6

TOP2i induce a time-dependent gene expression response in cardiomyocytes

A. Cormotif plot unedited

## B. Pie chart of motifs

C. Average absolute value of LFC by motif


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_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] broom_1.0.5         RColorBrewer_1.1-3  ggsignif_0.6.4     
 [4] cowplot_1.1.1       Cormotif_1.46.0     limma_3.56.2       
 [7] affy_1.78.2         Biobase_2.60.0      data.table_1.14.8  
[10] BiocGenerics_0.46.0 tinytex_0.45        lubridate_1.9.2    
[13] forcats_1.0.0       stringr_1.5.0       dplyr_1.1.2        
[16] purrr_1.0.1         readr_2.1.4         tidyr_1.3.0        
[19] tibble_3.2.1        ggplot2_3.4.2       tidyverse_2.0.0    
[22] car_3.1-2           carData_3.0-5       workflowr_1.7.0    

loaded via a namespace (and not attached):
 [1] gtable_0.3.3          xfun_0.39             bslib_0.5.0          
 [4] rstatix_0.7.2         processx_3.8.2        callr_3.7.3          
 [7] tzdb_0.4.0            vctrs_0.6.3           tools_4.3.1          
[10] ps_1.7.5              generics_0.1.3        fansi_1.0.4          
[13] highr_0.10            pkgconfig_2.0.3       lifecycle_1.0.3      
[16] farver_2.1.1          compiler_4.3.1        git2r_0.32.0         
[19] textshaping_0.3.6     munsell_0.5.0         getPass_0.2-2        
[22] httpuv_1.6.11         htmltools_0.5.5       sass_0.4.7           
[25] yaml_2.3.7            preprocessCore_1.62.1 ggpubr_0.6.0         
[28] later_1.3.1           pillar_1.9.0          jquerylib_0.1.4      
[31] whisker_0.4.1         cachem_1.0.8          abind_1.4-5          
[34] tidyselect_1.2.0      digest_0.6.33         stringi_1.7.12       
[37] labeling_0.4.2        rprojroot_2.0.3       fastmap_1.1.1        
[40] grid_4.3.1            colorspace_2.1-0      cli_3.6.1            
[43] magrittr_2.0.3        utf8_1.2.3            withr_2.5.0          
[46] backports_1.4.1       scales_1.2.1          promises_1.2.0.1     
[49] timechange_0.2.0      rmarkdown_2.23        httr_1.4.6           
[52] affyio_1.70.0         ragg_1.2.5            hms_1.1.3            
[55] evaluate_0.21         knitr_1.43            rlang_1.1.1          
[58] Rcpp_1.0.11           glue_1.6.2            BiocManager_1.30.21.1
[61] rstudioapi_0.15.0     jsonlite_1.8.7        R6_2.5.1             
[64] systemfonts_1.0.4     fs_1.6.3              zlibbioc_1.46.0