Last updated: 2023-04-10

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.


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.

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.

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.

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

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

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

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 d3f8cf7. 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/ACresponse_cluster24h.csv
    Ignored:    data/Clamp_Summary.csv
    Ignored:    data/Cormotif_24_k1-5_raw.RDS
    Ignored:    data/DAtable1.csv
    Ignored:    data/DDE_reQTL.txt
    Ignored:    data/DDEresp_list.csv
    Ignored:    data/DEG_cormotif.RDS
    Ignored:    data/DF_Plate_Peak.csv
    Ignored:    data/Da24counts.txt
    Ignored:    data/Dx24counts.txt
    Ignored:    data/Dx_reQTL_specific.txt
    Ignored:    data/Ep24counts.txt
    Ignored:    data/GOplots.R
    Ignored:    data/K_cluster
    Ignored:    data/K_cluster_kisthree.csv
    Ignored:    data/K_cluster_kistwo.csv
    Ignored:    data/Mt24counts.txt
    Ignored:    data/RINsamplelist.txt
    Ignored:    data/Seonane2019supp1.txt
    Ignored:    data/TOP2Bi-24hoursGO_analysis.csv
    Ignored:    data/TR24counts.txt
    Ignored:    data/Top2biresp_cluster24h.csv
    Ignored:    data/Viabilitylistfull.csv
    Ignored:    data/allexpressedgenes.txt
    Ignored:    data/allgenes.txt
    Ignored:    data/allmatrix.RDS
    Ignored:    data/avgLD50.RDS
    Ignored:    data/backGL.txt
    Ignored:    data/cormotif_3hk1-8.RDS
    Ignored:    data/cormotif_ER_respint.txt
    Ignored:    data/cormotif_ER_respset.txt
    Ignored:    data/cormotif_LR_respint.txt
    Ignored:    data/cormotif_LR_respset.txt
    Ignored:    data/cormotif_NRset.txt
    Ignored:    data/cormotif_TI_respint.txt
    Ignored:    data/cormotif_TI_respset.txt
    Ignored:    data/cormotif_initalK5.RDS
    Ignored:    data/cormotif_initialK5.RDS
    Ignored:    data/counts24hours.RDS
    Ignored:    data/cpmnorm_counts.csv
    Ignored:    data/dat_cpm.RDS
    Ignored:    data/data_outline.txt
    Ignored:    data/efit2results.RDS
    Ignored:    data/ensgtotal.txt
    Ignored:    data/filenameonly.txt
    Ignored:    data/filtered_cpm_counts.csv
    Ignored:    data/filtermatrix_x.RDS
    Ignored:    data/folder_05top/
    Ignored:    data/gene_prob_tran3h.RDS
    Ignored:    data/gene_probabilityk5.RDS
    Ignored:    data/individualDRCfile.RDS
    Ignored:    data/knowles56.GMT
    Ignored:    data/knowlesGMT.GMT
    Ignored:    data/mymatrix.RDS
    Ignored:    data/nonresponse_cluster24h.csv
    Ignored:    data/norm_LDH.csv
    Ignored:    data/norm_counts.csv
    Ignored:    data/plan2plot.png
    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/table3a.omar
    Ignored:    data/tvl24hour.txt
    Ignored:    data/tvl24hourw.txt
    Ignored:    data/venn_code.R

Untracked files:
    Untracked:  .RDataTmp
    Untracked:  .RDataTmp1
    Untracked:  code/extra_code.R
    Untracked:  output/output-old/
    Untracked:  reneebasecode.R

Unstaged changes:
    Modified:   analysis/DRC_analysis.Rmd
    Modified:   code/eQTLcodes.R
    Deleted:    output/Cormotif.svg
    Deleted:    output/Ctrxn24-3-23.svg
    Deleted:    output/Ctxnrate3-23.png
    Deleted:    output/Decay_Slope3-23.svg
    Deleted:    output/ERmotif5_LFC.svg
    Deleted:    output/GOBP_motif345.svg
    Deleted:    output/KEGGmotif_345.svg
    Deleted:    output/LD503-21-23.png
    Deleted:    output/LDH_24-3-23.svg
    Deleted:    output/LDH_243-23.svg
    Deleted:    output/LFCbytreatment3-25.svg
    Deleted:    output/LFCmotif4_LR.svg
    Deleted:    output/LR_RespMoti4.svg
    Deleted:    output/MeanAmp243-23.svg
    Deleted:    output/NRmotif1_LFC.svg
    Deleted:    output/Rise_Slope3-23.svg
    Deleted:    output/TI_LFC.svg
    Deleted:    output/TVLcorr3-23.svg
    Deleted:    output/TropI3-23.svg
    Deleted:    output/Venn24DEG-3-24.png
    Deleted:    output/motif1NR_LFC.svg
    Deleted:    output/motif3TIlfc3-25.svg
    Deleted:    output/motif4LR3-25LFC.svg
    Deleted:    output/motif5ER-LFC-3-25.svg
    Deleted:    output/nolegendLDH.svg
    Deleted:    output/resultsigVDA24.csv
    Deleted:    output/tropI_24-3-23.svg

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/run_all_analysis.Rmd) and HTML (docs/run_all_analysis.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 d3f8cf7 reneeisnowhere 2023-04-10 update push of new data
html f0a75e1 reneeisnowhere 2023-04-10 Build site.
Rmd 8ca4c7e reneeisnowhere 2023-04-10 first rmd commit
Rmd 2e69969 reneeisnowhere 2023-04-10 adding data
Rmd 0f1f1da reneeisnowhere 2023-04-10 final run analysis

This starts the documentation of the RNA-seq cardiotoxicity analysis for my manuscript

library(edgeR)#
library(limma)#
library(RColorBrewer)
library(mixOmics)
library(gridExtra)#
library(reshape2)#
#library(devtools)
library(AnnotationHub)
library(tidyverse)
library(scales)
library(biomaRt)#
library(Homo.sapiens)
library(cowplot)#
library(ggrepel)#
library(corrplot)
library(Hmisc)
 ###now we add genenames to the geneid###
 
geneid <- rownames(mymatrix) ### pulls the names we have in the counts file
genes <- select(Homo.sapiens, keys=geneid, columns=c("SYMBOL"),
  keytype="ENTREZID")
genes <- genes[!duplicated(genes$ENTREZID),]
mymatrix$genes <- genes
[1] 28395    72
[1] 14086    72



###  Vehicle 



###  Daunorubicin 



###  Doxorubicin 



###  Epirubicin 



###  Mitoxantrone 



###  Trastuzumab 

        samplenames indv         drug time RIN group       PC1      PC2
Da.1.3h MCW_RM_R_11    1 Daunorubicin   3h 9.3     1 -18.53902 62.11914
Do.1.3h MCW_RM_R_12    1  Doxorubicin   3h 9.8     2 -12.37874 73.96424
Ep.1.3h MCW_RM_R_13    1   Epirubicin   3h 9.8     3 -11.19226 66.47554
Mi.1.3h MCW_RM_R_14    1 Mitoxantrone   3h  10     4 -10.24538 73.46900
Tr.1.3h MCW_RM_R_15    1  Trastuzumab   3h 9.6     5 -12.21578 79.97646
Ve.1.3h MCW_RM_R_16    1      Vehicle   3h 9.9     6 -15.01396 76.61739
              PC3        PC4       PC5       PC6
Da.1.3h 44.793907  -4.229684  25.33474 -35.96203
Do.1.3h 24.565270  -8.522490 -19.86738 -19.00810
Ep.1.3h 33.103318  -9.146883  18.17321 -43.12911
Mi.1.3h 19.048074 -14.540036  -9.00047 -24.33769
Tr.1.3h  2.646249 -17.004856 -34.18428 -11.83222
Ve.1.3h 12.636907  -4.140009 -39.84065 -17.16481

  entrezgene_id ensembl_gene_id hgnc_symbol
1            88 ENSG00000077522       ACTN2
2           153 ENSG00000043591       ADRB1
3           154 ENSG00000169252       ADRB2
4           651 ENSG00000152785        BMP3
5           775 ENSG00000285479     CACNA1C
6     100874369 ENSG00000285479     CACNA1C

##correlation heatmap of counts matrix


R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

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    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] Hmisc_4.8-0                            
 [2] Formula_1.2-5                          
 [3] survival_3.5-3                         
 [4] corrplot_0.92                          
 [5] ggrepel_0.9.3                          
 [6] cowplot_1.1.1                          
 [7] Homo.sapiens_1.3.1                     
 [8] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [9] org.Hs.eg.db_3.15.0                    
[10] GO.db_3.15.0                           
[11] OrganismDbi_1.38.1                     
[12] GenomicFeatures_1.48.4                 
[13] GenomicRanges_1.48.0                   
[14] GenomeInfoDb_1.32.4                    
[15] AnnotationDbi_1.58.0                   
[16] IRanges_2.30.1                         
[17] S4Vectors_0.34.0                       
[18] Biobase_2.56.0                         
[19] biomaRt_2.52.0                         
[20] scales_1.2.1                           
[21] lubridate_1.9.2                        
[22] forcats_1.0.0                          
[23] stringr_1.5.0                          
[24] dplyr_1.1.0                            
[25] purrr_1.0.1                            
[26] readr_2.1.4                            
[27] tidyr_1.3.0                            
[28] tibble_3.1.8                           
[29] tidyverse_2.0.0                        
[30] AnnotationHub_3.4.0                    
[31] BiocFileCache_2.4.0                    
[32] dbplyr_2.3.1                           
[33] BiocGenerics_0.42.0                    
[34] reshape2_1.4.4                         
[35] gridExtra_2.3                          
[36] mixOmics_6.20.0                        
[37] ggplot2_3.4.1                          
[38] lattice_0.20-45                        
[39] MASS_7.3-58.2                          
[40] RColorBrewer_1.1-3                     
[41] edgeR_3.38.4                           
[42] limma_3.52.4                           
[43] workflowr_1.7.0                        

loaded via a namespace (and not attached):
  [1] backports_1.4.1               plyr_1.8.8                   
  [3] igraph_1.4.1                  splines_4.2.2                
  [5] BiocParallel_1.30.4           digest_0.6.31                
  [7] htmltools_0.5.4               fansi_1.0.4                  
  [9] checkmate_2.1.0               magrittr_2.0.3               
 [11] memoise_2.0.1                 cluster_2.1.4                
 [13] tzdb_0.3.0                    Biostrings_2.64.1            
 [15] matrixStats_0.63.0            rARPACK_0.11-0               
 [17] timechange_0.2.0              prettyunits_1.1.1            
 [19] jpeg_0.1-10                   colorspace_2.1-0             
 [21] blob_1.2.3                    rappdirs_0.3.3               
 [23] xfun_0.37                     callr_3.7.3                  
 [25] crayon_1.5.2                  RCurl_1.98-1.10              
 [27] jsonlite_1.8.4                graph_1.74.0                 
 [29] glue_1.6.2                    gtable_0.3.1                 
 [31] zlibbioc_1.42.0               XVector_0.36.0               
 [33] DelayedArray_0.22.0           DBI_1.1.3                    
 [35] Rcpp_1.0.10                   htmlTable_2.4.1              
 [37] xtable_1.8-4                  progress_1.2.2               
 [39] foreign_0.8-84                bit_4.0.5                    
 [41] htmlwidgets_1.6.1             httr_1.4.5                   
 [43] ellipsis_0.3.2                farver_2.1.1                 
 [45] pkgconfig_2.0.3               XML_3.99-0.13                
 [47] nnet_7.3-18                   deldir_1.0-6                 
 [49] sass_0.4.5                    locfit_1.5-9.7               
 [51] utf8_1.2.3                    labeling_0.4.2               
 [53] tidyselect_1.2.0              rlang_1.0.6                  
 [55] later_1.3.0                   munsell_0.5.0                
 [57] BiocVersion_3.15.2            tools_4.2.2                  
 [59] cachem_1.0.7                  cli_3.6.0                    
 [61] generics_0.1.3                RSQLite_2.3.0                
 [63] evaluate_0.20                 fastmap_1.1.1                
 [65] yaml_2.3.7                    processx_3.8.0               
 [67] knitr_1.42                    bit64_4.0.5                  
 [69] fs_1.6.1                      KEGGREST_1.36.3              
 [71] RBGL_1.72.0                   whisker_0.4.1                
 [73] mime_0.12                     xml2_1.3.3                   
 [75] compiler_4.2.2                rstudioapi_0.14              
 [77] filelock_1.0.2                curl_5.0.0                   
 [79] png_0.1-8                     interactiveDisplayBase_1.34.0
 [81] bslib_0.4.2                   stringi_1.7.12               
 [83] highr_0.10                    ps_1.7.2                     
 [85] RSpectra_0.16-1               Matrix_1.5-3                 
 [87] vctrs_0.5.2                   pillar_1.8.1                 
 [89] lifecycle_1.0.3               BiocManager_1.30.20          
 [91] jquerylib_0.1.4               data.table_1.14.8            
 [93] bitops_1.0-7                  corpcor_1.6.10               
 [95] httpuv_1.6.9                  rtracklayer_1.56.1           
 [97] latticeExtra_0.6-30           R6_2.5.1                     
 [99] BiocIO_1.6.0                  promises_1.2.0.1             
[101] codetools_0.2-19              SummarizedExperiment_1.26.1  
[103] rprojroot_2.0.3               rjson_0.2.21                 
[105] withr_2.5.0                   GenomicAlignments_1.32.1     
[107] Rsamtools_2.12.0              GenomeInfoDbData_1.2.8       
[109] parallel_4.2.2                hms_1.1.2                    
[111] rpart_4.1.19                  grid_4.2.2                   
[113] rmarkdown_2.20                MatrixGenerics_1.8.1         
[115] git2r_0.31.0                  getPass_0.2-2                
[117] base64enc_0.1-3               shiny_1.7.4                  
[119] ellipse_0.4.3                 interp_1.1-3                 
[121] restfulr_0.0.15