From a5303119574207f0fea751dcb26f5ddf1a9b05ea Mon Sep 17 00:00:00 2001 From: travis-m-blimkie Date: Mon, 20 Nov 2023 17:54:55 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20travis-m?= =?UTF-8?q?-blimkie/tRavis@d95eaf3eb3458af970992916962c1cc3a17e0761=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 8 +- LICENSE-text.html | 8 +- articles/extra.html | 224 ++++++++++++++++++ .../figure-html/unnamed-chunk-3-1.png | Bin 0 -> 34495 bytes articles/index.html | 12 +- articles/tRavis.html | 34 +-- authors.html | 12 +- index.html | 8 +- pkgdown.yml | 3 +- reference/biomart_id_mapping_human.html | 8 +- reference/biomart_id_mapping_mouse.html | 8 +- reference/index.html | 8 +- reference/reactome_categories_human.html | 8 +- reference/reactome_categories_mouse.html | 8 +- reference/tr_anno_cleaner.html | 8 +- reference/tr_clean_deseq2_result.html | 8 +- reference/tr_compare_lists.html | 8 +- reference/tr_get_files.html | 8 +- reference/tr_qc_plots.html | 8 +- reference/tr_sort_alphanum.html | 8 +- reference/tr_test_enrichment.html | 10 +- reference/tr_theme.html | 8 +- reference/tr_tidy_gage.html | 8 +- reference/tr_trunc_neatly.html | 8 +- search.json | 2 +- sitemap.xml | 3 + 26 files changed, 396 insertions(+), 40 deletions(-) create mode 100644 articles/extra.html create mode 100644 articles/extra_files/figure-html/unnamed-chunk-3-1.png diff --git a/404.html b/404.html index a22d4c8..c6a7bad 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ tRavis - 0.73.19 + 0.73.20 + + + + + +
+ + + + +
+
+ + + +
+library(tRavis)
+#> Thanks for using tRavis v0.73.20! If you encounter any bugs
+#> or problems, please submit an issue at the Github page:
+#> https://github.com/travis-m-blimkie/tRavis/issues
+
+

Extra examples +

+
+

tr_clean_deseq_results +

+
+ex_deseq_results <- 
+  readRDS(system.file("extdata", "ex_deseq_results.rds", package = "tRavis"))
+ex_deseq_results
+#> log2 fold change (MLE): condition B vs A 
+#> Wald test p-value: condition B vs A 
+#> DataFrame with 200 rows and 6 columns
+#>          baseMean log2FoldChange     lfcSE      stat      pvalue        padj
+#>         <numeric>      <numeric> <numeric> <numeric>   <numeric>   <numeric>
+#> gene1      7.1530      -0.636105  0.750697 -0.847352 3.96799e-01 4.95998e-01
+#> gene2    108.3659       2.872486  0.357737  8.029601 9.77899e-16 1.62983e-14
+#> gene3     25.1923       1.724502  0.643106  2.681522 7.32882e-03 1.62863e-02
+#> gene4    110.2302      -1.375727  0.321775 -4.275440 1.90761e-05 7.06521e-05
+#> gene5     15.1829      -5.412610  0.819823 -6.602166 4.05195e-11 3.68359e-10
+#> ...           ...            ...       ...       ...         ...         ...
+#> gene196   1.28627      -0.654713  1.676396 -0.390548 6.96131e-01 7.86589e-01
+#> gene197 591.21368       3.285941  0.278768 11.787369 4.53489e-32 4.53489e-30
+#> gene198   4.67660       2.434828  0.961683  2.531839 1.13466e-02 2.33951e-02
+#> gene199  14.96302      -2.313151  0.491582 -4.705521 2.53218e-06 1.17776e-05
+#> gene200  17.69265       1.970386  0.602859  3.268401 1.08157e-03 3.00436e-03
+
+tr_clean_deseq2_result(ex_deseq_results, p_adjusted = 0.1, fold_change = 2)
+#> Found 110 DE genes for condition B vs A.
+#> # A tibble: 110 × 7
+#>    gene    baseMean log2FoldChange lfcSE   stat   pvalue     padj
+#>    <chr>      <dbl>          <dbl> <dbl>  <dbl>    <dbl>    <dbl>
+#>  1 gene95     853.            3.35 0.279  12.0  3.26e-33 6.53e-31
+#>  2 gene197    591.            3.29 0.279  11.8  4.53e-32 4.53e-30
+#>  3 gene180    420.            3.30 0.298  11.1  1.57e-28 1.05e-26
+#>  4 gene70     235.           -2.91 0.276 -10.5  5.23e-26 2.62e-24
+#>  5 gene106    886.            3.08 0.303  10.1  3.80e-24 1.52e-22
+#>  6 gene187     57.3          -4.28 0.428 -10.0  1.42e-23 4.74e-22
+#>  7 gene26      93.9           4.62 0.473   9.77 1.47e-22 4.20e-21
+#>  8 gene68      72.7          -3.23 0.345  -9.37 7.58e-21 1.90e-19
+#>  9 gene122    462.            2.63 0.307   8.58 9.79e-18 2.18e-16
+#> 10 gene39     191.            2.67 0.325   8.20 2.33e-16 4.66e-15
+#> # ℹ 100 more rows
+
+
+

tr_theme +

+
+library(ggplot2)
+
+ggplot(mtcars, aes(as.factor(cyl), mpg)) + 
+  geom_boxplot() + 
+  tr_theme(base_family = "Helvetica", base_size = 20)
+

+
+
+
+

Session information +

+
#> R version 4.3.2 (2023-10-31)
+#> Platform: x86_64-pc-linux-gnu (64-bit)
+#> Running under: Ubuntu 22.04.3 LTS
+#> 
+#> Matrix products: default
+#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
+#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
+#> 
+#> locale:
+#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
+#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
+#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
+#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
+#> 
+#> time zone: UTC
+#> tzcode source: system (glibc)
+#> 
+#> attached base packages:
+#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
+#> [8] base     
+#> 
+#> other attached packages:
+#>  [1] ggplot2_3.4.4               DESeq2_1.40.2              
+#>  [3] SummarizedExperiment_1.30.2 Biobase_2.60.0             
+#>  [5] MatrixGenerics_1.12.3       matrixStats_1.1.0          
+#>  [7] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
+#>  [9] IRanges_2.34.1              S4Vectors_0.38.2           
+#> [11] BiocGenerics_0.46.0         tRavis_0.73.20             
+#> 
+#> loaded via a namespace (and not attached):
+#>  [1] tidyselect_1.2.0        viridisLite_0.4.2       dplyr_1.1.4            
+#>  [4] farver_2.1.1            bitops_1.0-7            fastmap_1.1.1          
+#>  [7] lazyeval_0.2.2          RCurl_1.98-1.13         janitor_2.2.0          
+#> [10] digest_0.6.33           timechange_0.2.0        lifecycle_1.0.4        
+#> [13] magrittr_2.0.3          compiler_4.3.2          rlang_1.1.2            
+#> [16] sass_0.4.7              tools_4.3.2             utf8_1.2.4             
+#> [19] yaml_2.3.7              data.table_1.14.8       knitr_1.45             
+#> [22] S4Arrays_1.0.6          labeling_0.4.3          htmlwidgets_1.6.2      
+#> [25] DelayedArray_0.26.7     abind_1.4-5             BiocParallel_1.34.2    
+#> [28] withr_2.5.2             purrr_1.0.2             desc_1.4.2             
+#> [31] grid_4.3.2              fansi_1.0.5             colorspace_2.1-0       
+#> [34] scales_1.2.1            cli_3.6.1               rmarkdown_2.25         
+#> [37] crayon_1.5.2            ragg_1.2.6              generics_0.1.3         
+#> [40] httr_1.4.7              tzdb_0.4.0              rjson_0.2.21           
+#> [43] cachem_1.0.8            stringr_1.5.1           zlibbioc_1.46.0        
+#> [46] parallel_4.3.2          XVector_0.40.0          vctrs_0.6.4            
+#> [49] Matrix_1.6-1.1          jsonlite_1.8.7          hms_1.1.3              
+#> [52] systemfonts_1.0.5       locfit_1.5-9.8          plotly_4.10.3          
+#> [55] tidyr_1.3.0             jquerylib_0.1.4         glue_1.6.2             
+#> [58] pkgdown_2.0.7           codetools_0.2-19        lubridate_1.9.3        
+#> [61] stringi_1.8.1           gtable_0.3.4            munsell_0.5.0          
+#> [64] tibble_3.2.1            pillar_1.9.0            htmltools_0.5.7        
+#> [67] GenomeInfoDbData_1.2.10 R6_2.5.1                textshaping_0.3.7      
+#> [70] rprojroot_2.0.4         evaluate_0.23           lattice_0.21-9         
+#> [73] readr_2.1.4             highr_0.10              memoise_2.0.1          
+#> [76] snakecase_0.11.1        bslib_0.5.1             Rcpp_1.0.11            
+#> [79] xfun_0.41               fs_1.6.3                pkgconfig_2.0.3
+
+
+
+ + + +
+ + + +
+
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