From d12273be55d2f3eac9e49ef6342a19dfad83ad84 Mon Sep 17 00:00:00 2001 From: Anka Date: Thu, 9 Jan 2025 21:31:22 +0000 Subject: [PATCH] Built site for GeneTonic@3.1.1: 626ac9a --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- LICENSE-text.html | 2 +- LICENSE.html | 2 +- articles/GeneTonic_manual.html | 144 +++++++++--------- articles/index.html | 2 +- authors.html | 2 +- index.html | 2 +- news/index.html | 10 +- pkgdown.yml | 4 +- reference/GeneTonic-pkg.html | 2 +- reference/GeneTonic.html | 2 +- reference/GeneTonicList.html | 2 +- reference/check_colors.html | 2 +- reference/checkup_GeneTonic.html | 2 +- reference/checkup_gtl.html | 2 +- reference/cluster_markov.html | 2 +- reference/create_jaccard_matrix.html | 2 +- reference/create_kappa_matrix.html | 2 +- reference/create_upsetdata.html | 2 +- reference/deprecated.html | 2 +- reference/describe_gtl.html | 2 +- reference/deseqresult2df.html | 2 +- reference/distill_enrichment.html | 6 +- reference/dot-check_pandoc.html | 2 +- reference/editor_to_vector_sanitized.html | 2 +- reference/enhance_table.html | 2 +- reference/enrichment_map.html | 6 +- reference/enrichr_output_macrophage.html | 2 +- reference/export_for_iSEE.html | 6 +- reference/export_to_sif.html | 4 +- reference/fgseaRes.html | 2 +- reference/gene_plot.html | 7 +- reference/geneinfo_2_html.html | 2 +- reference/get_aggrscores.html | 2 +- reference/get_expression_values.html | 2 +- reference/ggs_backbone.html | 2 +- reference/ggs_graph.html | 8 +- reference/go_2_html.html | 2 +- reference/gostres_macrophage.html | 2 +- reference/gs_alluvial.html | 6 +- reference/gs_dendro.html | 2 +- reference/gs_fuzzyclustering.html | 2 +- reference/gs_heatmap.html | 2 +- reference/gs_horizon.html | 2 +- reference/gs_mds.html | 2 +- reference/gs_radar.html | 8 +- reference/gs_scores.html | 2 +- reference/gs_scoresheat.html | 2 +- reference/gs_simplify.html | 2 +- reference/gs_summary_heat.html | 2 +- reference/gs_summary_overview.html | 2 +- reference/gs_summary_overview_pair.html | 2 +- reference/gs_upset.html | 2 +- reference/gs_volcano.html | 2 +- reference/happy_hour.html | 2 +- reference/index.html | 2 +- reference/map2color.html | 4 +- reference/overlap_coefficient.html | 2 +- reference/overlap_jaccard_index.html | 2 +- reference/res_macrophage_IFNg_vs_naive.html | 2 +- reference/shake_davidResult.html | 2 +- reference/shake_enrichResult.html | 2 +- reference/shake_enrichrResult.html | 2 +- reference/shake_fgseaResult.html | 2 +- reference/shake_gprofilerResult.html | 2 +- reference/shake_gsenrichResult.html | 2 +- reference/shake_topGOtableResult.html | 2 +- reference/signature_volcano.html | 4 +- reference/styleColorBar_divergent.html | 2 +- reference/summarize_ggs_hubgenes.html | 2 +- .../topgoDE_macrophage_IFNg_vs_naive.html | 2 +- 72 files changed, 172 insertions(+), 163 deletions(-) diff --git a/404.html b/404.html index 005ac30..9934a0e 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 608dc05..830337e 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/LICENSE-text.html b/LICENSE-text.html index 481193b..474df69 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/LICENSE.html b/LICENSE.html index c20bab6..44f1c17 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/articles/GeneTonic_manual.html b/articles/GeneTonic_manual.html index 4708c1a..b1df816 100644 --- a/articles/GeneTonic_manual.html +++ b/articles/GeneTonic_manual.html @@ -34,7 +34,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -112,7 +112,7 @@

Annekathrin (IMBEI), Mainz
-

16 December 2024

+

9 January 2025

Source: vignettes/GeneTonic_manual.Rmd @@ -126,7 +126,7 @@

16 December 2024

font-size: 10px } -

Compiled date: 2024-12-16

+

Compiled date: 2025-01-09

Last edited: 2022-04-04

License: MIT + file LICENSE

@@ -789,7 +789,7 @@

Overview functions: genes and ge library("plotly") ggplotly(p)
-

Display the relationship between genesets and genes that belong to +

Display the relationship between genesets and genes that belong to them (useful e.g. to see overlap between terms):

 gs_alluvial(res_enrich = res_enrich_macrophage,
@@ -797,7 +797,7 @@ 
Overview functions: genes and ge
             annotation_obj = anno_df,
             n_gs = 4)
-

Display a bipartite graph where genesets and genes are included, and +

Display a bipartite graph where genesets and genes are included, and make it interactive:

 ggs <- ggs_graph(res_enrich_macrophage,
@@ -805,9 +805,9 @@ 
Overview functions: genes and ge
                  anno_df,
                  n_gs = 20)
 ggs
-#> IGRAPH 4157257 UN-- 266 656 -- 
+#> IGRAPH d3cb532 UN-- 266 656 -- 
 #> + attr: name (v/c), nodetype (v/c), shape (v/c), color (v/c), title (v/c)
-#> + edges from 4157257 (vertex names):
+#> + edges from d3cb532 (vertex names):
 #>  [1] adaptive immune response--B2M     adaptive immune response--BCL6   
 #>  [3] adaptive immune response--BTN3A1  adaptive immune response--BTN3A2 
 #>  [5] adaptive immune response--BTN3A3  adaptive immune response--C1QB   
@@ -828,7 +828,7 @@ 
Overview functions: genes and ge
                                      hover = TRUE),
              nodesIdSelection = TRUE)
- +

Summary representations @@ -1139,12 +1139,12 @@

Comparison between sets# with only one set gs_radar(res_enrich = res_enrich_macrophage)

-
+
 # with a dataset to compare against
 gs_radar(res_enrich = res_enrich_macrophage,
          res_enrich2 = res_enrich2)

 

-
In particular, the gs_horizon function tries to group
+
In particular, the gs_horizon function tries to group
 the different genesets based on their relative enrichment across
 conditions, similar to a representation of (Dutertre et al. 2019) (e.g. Fig. 5G). Thanks to
 Charlotte Soneson for providing a compact working implementation of
@@ -1334,9 +1334,9 @@ 
Session Info
 
 sessionInfo()
-#> R Under development (unstable) (2024-12-13 r87441)
+#> R Under development (unstable) (2025-01-03 r87521)
 #> Platform: aarch64-apple-darwin20
-#> Running under: macOS Sonoma 14.7.1
+#> Running under: macOS Sonoma 14.7.2
 #> 
 #> Matrix products: default
 #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
@@ -1352,74 +1352,74 @@ 
Session Info#> [1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#>  [1] igraph_2.1.2                magrittr_2.0.3              visNetwork_2.1.2           
+#>  [1] igraph_2.1.3                magrittr_2.0.3              visNetwork_2.1.2           
 #>  [4] plotly_4.10.4               ggplot2_3.5.1               org.Hs.eg.db_3.20.0        
 #>  [7] AnnotationDbi_1.69.0        DESeq2_1.47.1               SummarizedExperiment_1.37.0
-#> [10] Biobase_2.67.0              MatrixGenerics_1.19.0       matrixStats_1.4.1          
+#> [10] Biobase_2.67.0              MatrixGenerics_1.19.0       matrixStats_1.5.0          
 #> [13] GenomicRanges_1.59.1        GenomeInfoDb_1.43.2         IRanges_2.41.2             
 #> [16] S4Vectors_0.45.2            BiocGenerics_0.53.3         generics_0.1.3             
-#> [19] macrophage_1.23.0           GeneTonic_3.1.0             BiocStyle_2.35.0           
+#> [19] macrophage_1.23.0           GeneTonic_3.1.1             BiocStyle_2.35.0           
 #> 
 #> loaded via a namespace (and not attached):
-#>   [1] fs_1.6.5                 bitops_1.0-9             enrichplot_1.27.3       
+#>   [1] fs_1.6.5                 bitops_1.0-9             enrichplot_1.27.4       
 #>   [4] fontawesome_0.5.3        httr_1.4.7               RColorBrewer_1.1-3      
 #>   [7] doParallel_1.0.17        dynamicTreeCut_1.63-1    tippy_0.1.0             
-#>  [10] tools_4.5.0              utf8_1.2.4               R6_2.5.1                
-#>  [13] DT_0.33                  lazyeval_0.2.2           mgcv_1.9-1              
-#>  [16] GetoptLong_1.0.5         withr_3.0.2              prettyunits_1.2.0       
-#>  [19] gridExtra_2.3            cli_3.6.3                textshaping_0.4.1       
-#>  [22] labeling_0.4.3           sass_0.4.9               topGO_2.59.0            
-#>  [25] bs4Dash_2.3.4            ggridges_0.5.6           goseq_1.59.0            
-#>  [28] pkgdown_2.1.1.9000       Rsamtools_2.23.1         systemfonts_1.1.0       
-#>  [31] yulab.utils_0.1.8        gson_0.1.0               txdbmaker_1.3.1         
-#>  [34] DOSE_4.1.0               R.utils_2.12.3           RSQLite_2.3.9           
-#>  [37] gridGraphics_0.5-1       shape_1.4.6.1            BiocIO_1.17.1           
-#>  [40] crosstalk_1.2.1          dplyr_1.1.4              dendextend_1.19.0       
-#>  [43] GO.db_3.20.0             Matrix_1.7-1             fansi_1.0.6             
-#>  [46] abind_1.4-8              R.methodsS3_1.8.2        lifecycle_1.0.4         
-#>  [49] yaml_2.3.10              qvalue_2.39.0            SparseArray_1.7.2       
-#>  [52] BiocFileCache_2.15.0     grid_4.5.0               blob_1.2.4              
-#>  [55] promises_1.3.2           crayon_1.5.3             miniUI_0.1.1.1          
-#>  [58] ggtangle_0.0.5           lattice_0.22-6           ComplexUpset_1.3.6      
-#>  [61] cowplot_1.1.3            GenomicFeatures_1.59.1   KEGGREST_1.47.0         
-#>  [64] pillar_1.9.0             knitr_1.49               ComplexHeatmap_2.23.0   
-#>  [67] fgsea_1.33.0             rjson_0.2.23             codetools_0.2-20        
-#>  [70] fastmatch_1.1-4          glue_1.8.0               ggfun_0.1.8             
-#>  [73] data.table_1.16.4        vctrs_0.6.5              png_0.1-8               
-#>  [76] treeio_1.31.0            gtable_0.3.6             cachem_1.1.0            
-#>  [79] xfun_0.49                S4Arrays_1.7.1           mime_0.12               
-#>  [82] iterators_1.0.14         nlme_3.1-166             ggtree_3.15.0           
-#>  [85] bit64_4.5.2              progress_1.2.3           filelock_1.0.3          
-#>  [88] bslib_0.8.0              colorspace_2.1-1         DBI_1.2.3               
-#>  [91] tidyselect_1.2.1         bit_4.5.0.1              compiler_4.5.0          
-#>  [94] curl_6.0.1               httr2_1.0.7              graph_1.85.0            
-#>  [97] BiasedUrn_2.0.12         SparseM_1.84-2           expm_1.0-0              
-#> [100] xml2_1.3.6               desc_1.4.3               DelayedArray_0.33.3     
-#> [103] colourpicker_1.3.0       bookdown_0.41            rtracklayer_1.67.0      
-#> [106] scales_1.3.0             mosdef_1.3.0             rappdirs_0.3.3          
-#> [109] stringr_1.5.1            digest_0.6.37            rmarkdown_2.29          
-#> [112] XVector_0.47.0           htmltools_0.5.8.1        pkgconfig_2.0.3         
-#> [115] dbplyr_2.5.0             fastmap_1.2.0            rlang_1.1.4             
-#> [118] GlobalOptions_0.1.2      htmlwidgets_1.6.4        UCSC.utils_1.3.0        
-#> [121] shiny_1.10.0             farver_2.1.2             jquerylib_0.1.4         
-#> [124] jsonlite_1.8.9           BiocParallel_1.41.0      GOSemSim_2.33.0         
-#> [127] R.oo_1.27.0              RCurl_1.98-1.16          GenomeInfoDbData_1.2.13 
-#> [130] ggplotify_0.1.2          patchwork_1.3.0          munsell_0.5.1           
-#> [133] Rcpp_1.0.13-1            ape_5.8-1                shinycssloaders_1.1.0   
-#> [136] viridis_0.6.5            stringi_1.8.4            rintrojs_0.3.4          
-#> [139] zlibbioc_1.53.0          MASS_7.3-61              plyr_1.8.9              
-#> [142] parallel_4.5.0           ggrepel_0.9.6            Biostrings_2.75.3       
-#> [145] splines_4.5.0            hms_1.1.3                geneLenDataBase_1.43.0  
-#> [148] circlize_0.4.16          locfit_1.5-9.10          reshape2_1.4.4          
-#> [151] biomaRt_2.63.0           XML_3.99-0.17            evaluate_1.0.1          
-#> [154] BiocManager_1.30.25      foreach_1.5.2            tweenr_2.0.3            
-#> [157] httpuv_1.6.15            backbone_2.1.4           tidyr_1.3.1             
-#> [160] purrr_1.0.2              polyclip_1.10-7          clue_0.3-66             
-#> [163] ggforce_0.4.2            xtable_1.8-4             restfulr_0.0.15         
-#> [166] tidytree_0.4.6           later_1.4.1              viridisLite_0.4.2       
-#> [169] ragg_1.3.3               tibble_3.2.1             clusterProfiler_4.15.1  
-#> [172] aplot_0.2.3              memoise_2.0.1            GenomicAlignments_1.43.0
-#> [175] cluster_2.1.8            shinyWidgets_0.8.7       shinyAce_0.4.3

+#>  [10] tools_4.5.0              R6_2.5.1                 DT_0.33                 
+#>  [13] lazyeval_0.2.2           mgcv_1.9-1               GetoptLong_1.0.5        
+#>  [16] withr_3.0.2              prettyunits_1.2.0        gridExtra_2.3           
+#>  [19] cli_3.6.3                textshaping_0.4.1        labeling_0.4.3          
+#>  [22] sass_0.4.9               topGO_2.59.0             bs4Dash_2.3.4           
+#>  [25] ggridges_0.5.6           goseq_1.59.0             pkgdown_2.1.1.9000      
+#>  [28] Rsamtools_2.23.1         systemfonts_1.1.0        yulab.utils_0.1.9       
+#>  [31] gson_0.1.0               txdbmaker_1.3.1          DOSE_4.1.0              
+#>  [34] R.utils_2.12.3           RSQLite_2.3.9            gridGraphics_0.5-1      
+#>  [37] shape_1.4.6.1            BiocIO_1.17.1            crosstalk_1.2.1         
+#>  [40] dplyr_1.1.4              dendextend_1.19.0        GO.db_3.20.0            
+#>  [43] Matrix_1.7-1             abind_1.4-8              R.methodsS3_1.8.2       
+#>  [46] lifecycle_1.0.4          yaml_2.3.10              qvalue_2.39.0           
+#>  [49] SparseArray_1.7.2        BiocFileCache_2.15.0     grid_4.5.0              
+#>  [52] blob_1.2.4               promises_1.3.2           crayon_1.5.3            
+#>  [55] miniUI_0.1.1.1           ggtangle_0.0.6           lattice_0.22-6          
+#>  [58] ComplexUpset_1.3.6       cowplot_1.1.3            GenomicFeatures_1.59.1  
+#>  [61] KEGGREST_1.47.0          pillar_1.10.1            knitr_1.49              
+#>  [64] ComplexHeatmap_2.23.0    fgsea_1.33.2             rjson_0.2.23            
+#>  [67] codetools_0.2-20         fastmatch_1.1-6          glue_1.8.0              
+#>  [70] ggfun_0.1.8              data.table_1.16.4        vctrs_0.6.5             
+#>  [73] png_0.1-8                treeio_1.31.0            gtable_0.3.6            
+#>  [76] cachem_1.1.0             xfun_0.50                S4Arrays_1.7.1          
+#>  [79] mime_0.12                iterators_1.0.14         nlme_3.1-166            
+#>  [82] ggtree_3.15.0            bit64_4.5.2              progress_1.2.3          
+#>  [85] filelock_1.0.3           bslib_0.8.0              colorspace_2.1-1        
+#>  [88] DBI_1.2.3                tidyselect_1.2.1         bit_4.5.0.1             
+#>  [91] compiler_4.5.0           curl_6.1.0               httr2_1.0.7             
+#>  [94] graph_1.85.1             BiasedUrn_2.0.12         SparseM_1.84-2          
+#>  [97] expm_1.0-0               xml2_1.3.6               desc_1.4.3              
+#> [100] DelayedArray_0.33.3      colourpicker_1.3.0       bookdown_0.42           
+#> [103] rtracklayer_1.67.0       scales_1.3.0             mosdef_1.3.1            
+#> [106] rappdirs_0.3.3           stringr_1.5.1            digest_0.6.37           
+#> [109] rmarkdown_2.29           XVector_0.47.2           htmltools_0.5.8.1       
+#> [112] pkgconfig_2.0.3          dbplyr_2.5.0             fastmap_1.2.0           
+#> [115] rlang_1.1.4              GlobalOptions_0.1.2      htmlwidgets_1.6.4       
+#> [118] UCSC.utils_1.3.0         shiny_1.10.0             farver_2.1.2            
+#> [121] jquerylib_0.1.4          jsonlite_1.8.9           BiocParallel_1.41.0     
+#> [124] GOSemSim_2.33.0          R.oo_1.27.0              RCurl_1.98-1.16         
+#> [127] GenomeInfoDbData_1.2.13  ggplotify_0.1.2          patchwork_1.3.0         
+#> [130] munsell_0.5.1            Rcpp_1.0.13-1            ape_5.8-1               
+#> [133] shinycssloaders_1.1.0    viridis_0.6.5            stringi_1.8.4           
+#> [136] rintrojs_0.3.4           zlibbioc_1.53.0          MASS_7.3-64             
+#> [139] plyr_1.8.9               parallel_4.5.0           ggrepel_0.9.6           
+#> [142] Biostrings_2.75.3        splines_4.5.0            hms_1.1.3               
+#> [145] geneLenDataBase_1.43.0   circlize_0.4.16          locfit_1.5-9.10         
+#> [148] reshape2_1.4.4           biomaRt_2.63.0           XML_3.99-0.18           
+#> [151] evaluate_1.0.1           BiocManager_1.30.25      foreach_1.5.2           
+#> [154] tweenr_2.0.3             httpuv_1.6.15            backbone_2.1.4          
+#> [157] tidyr_1.3.1              purrr_1.0.2              polyclip_1.10-7         
+#> [160] clue_0.3-66              ggforce_0.4.2            xtable_1.8-4            
+#> [163] restfulr_0.0.15          tidytree_0.4.6           later_1.4.1             
+#> [166] viridisLite_0.4.2        ragg_1.3.3               tibble_3.2.1            
+#> [169] clusterProfiler_4.15.1   aplot_0.2.4              memoise_2.0.1           
+#> [172] GenomicAlignments_1.43.0 cluster_2.1.8            shinyWidgets_0.8.7      
+#> [175] shinyAce_0.4.3

References diff --git a/articles/index.html b/articles/index.html index 41cfe37..82c3482 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1

diff --git a/authors.html b/authors.html index c032f51..cc8e359 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/index.html b/index.html index edae876..f67a58a 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/news/index.html b/news/index.html index d94c0d9..cb3b9f3 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -64,6 +64,14 @@

Changelog

Source: NEWS.md +
+

GeneTonic 3.2.0

+
+

Other notes

+
  • +gene_plot() defaults now to NULL in the intgroup parameter, which translates into using the first colData item
    • +
+

GeneTonic 2.99.0

diff --git a/pkgdown.yml b/pkgdown.yml index 972af98..c31b5ed 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,6 +1,6 @@ pandoc: 3.1.11 pkgdown: 2.1.1.9000 -pkgdown_sha: 5c03b7444923f7c797b8b283e175f8eed63797a7 +pkgdown_sha: 6615322cb2ce15b1effcecf894123c88fa10b9c9 articles: GeneTonic_manual: GeneTonic_manual.html -last_built: 2024-12-16T18:57Z +last_built: 2025-01-09T21:29Z diff --git a/reference/GeneTonic-pkg.html b/reference/GeneTonic-pkg.html index a83fb58..af51287 100644 --- a/reference/GeneTonic-pkg.html +++ b/reference/GeneTonic-pkg.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1
diff --git a/reference/GeneTonic.html b/reference/GeneTonic.html index 095b144..ca767c2 100644 --- a/reference/GeneTonic.html +++ b/reference/GeneTonic.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1
diff --git a/reference/GeneTonicList.html b/reference/GeneTonicList.html index 9001ac5..3ae79c7 100644 --- a/reference/GeneTonicList.html +++ b/reference/GeneTonicList.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/check_colors.html b/reference/check_colors.html index 0a8b101..ed2129f 100644 --- a/reference/check_colors.html +++ b/reference/check_colors.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/checkup_GeneTonic.html b/reference/checkup_GeneTonic.html index 259d184..0fa3f88 100644 --- a/reference/checkup_GeneTonic.html +++ b/reference/checkup_GeneTonic.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/checkup_gtl.html b/reference/checkup_gtl.html index 088c54b..e399aab 100644 --- a/reference/checkup_gtl.html +++ b/reference/checkup_gtl.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/cluster_markov.html b/reference/cluster_markov.html index 8ae105f..d36ac77 100644 --- a/reference/cluster_markov.html +++ b/reference/cluster_markov.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/create_jaccard_matrix.html b/reference/create_jaccard_matrix.html index c50c0cc..6b882c8 100644 --- a/reference/create_jaccard_matrix.html +++ b/reference/create_jaccard_matrix.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/create_kappa_matrix.html b/reference/create_kappa_matrix.html index 90141bb..d2627e8 100644 --- a/reference/create_kappa_matrix.html +++ b/reference/create_kappa_matrix.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/create_upsetdata.html b/reference/create_upsetdata.html index acfb91c..a813fb3 100644 --- a/reference/create_upsetdata.html +++ b/reference/create_upsetdata.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/deprecated.html b/reference/deprecated.html index bfa6f71..8bc3e78 100644 --- a/reference/deprecated.html +++ b/reference/deprecated.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/describe_gtl.html b/reference/describe_gtl.html index 8b7355d..a76e59c 100644 --- a/reference/describe_gtl.html +++ b/reference/describe_gtl.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/deseqresult2df.html b/reference/deseqresult2df.html index db6328e..c802b12 100644 --- a/reference/deseqresult2df.html +++ b/reference/deseqresult2df.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/distill_enrichment.html b/reference/distill_enrichment.html index 83a9d29..30c97cc 100644 --- a/reference/distill_enrichment.html +++ b/reference/distill_enrichment.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -181,11 +181,11 @@

Examples

#> [4] "metags_n_genes" "metags_gsidlist" "metags_gsdesclist" #> [7] "metags_msgs" "metags_mcgs" distilled$distilled_em -#> IGRAPH d0fcce6 UN-- 100 553 -- +#> IGRAPH 4842756 UN-- 100 553 -- #> + attr: name (v/c), size (v/n), original_size (v/n), color.background #> | (v/c), color.highlight (v/c), color.hover (v/c), color.border (v/c), #> | membership (v/n), color (v/n), width (e/n), color (e/c) -#> + edges from d0fcce6 (vertex names): +#> + edges from 4842756 (vertex names): #> [1] adaptive immune response--interferon-gamma-mediated signaling pathway #> [2] adaptive immune response--antigen processing and presentation of endogenous peptide antigen via MHC class I #> [3] adaptive immune response--positive regulation of T cell mediated cytotoxicity diff --git a/reference/dot-check_pandoc.html b/reference/dot-check_pandoc.html index 80a523d..ae1cb80 100644 --- a/reference/dot-check_pandoc.html +++ b/reference/dot-check_pandoc.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/editor_to_vector_sanitized.html b/reference/editor_to_vector_sanitized.html index 505cef6..61be6cb 100644 --- a/reference/editor_to_vector_sanitized.html +++ b/reference/editor_to_vector_sanitized.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/enhance_table.html b/reference/enhance_table.html index 5985b03..83f82b3 100644 --- a/reference/enhance_table.html +++ b/reference/enhance_table.html @@ -19,7 +19,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/enrichment_map.html b/reference/enrichment_map.html index 2da5137..7fcd204 100644 --- a/reference/enrichment_map.html +++ b/reference/enrichment_map.html @@ -20,7 +20,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -202,11 +202,11 @@

Examples

) em -#> IGRAPH 311a859 UN-- 20 54 -- +#> IGRAPH 65e2e63 UN-- 20 54 -- #> + attr: name (v/c), size (v/n), original_size (v/n), color.background #> | (v/c), color.highlight (v/c), color.hover (v/c), color.border (v/c), #> | width (e/n), color (e/c) -#> + edges from 311a859 (vertex names): +#> + edges from 65e2e63 (vertex names): #> [1] adaptive immune response--interferon-gamma-mediated signaling pathway #> [2] adaptive immune response--antigen processing and presentation of endogenous peptide antigen via MHC class I #> [3] adaptive immune response--positive regulation of T cell mediated cytotoxicity diff --git a/reference/enrichr_output_macrophage.html b/reference/enrichr_output_macrophage.html index 2dee3b7..0bfa327 100644 --- a/reference/enrichr_output_macrophage.html +++ b/reference/enrichr_output_macrophage.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/export_for_iSEE.html b/reference/export_for_iSEE.html index f87f1f6..64e7866 100644 --- a/reference/export_for_iSEE.html +++ b/reference/export_for_iSEE.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -78,11 +78,11 @@

Arguments

dds
-

A DESeqDataSet object.

+

A DESeq2::DESeqDataSet() object.

res_de
-

A DESeqResults object.

+

A DESeq2::DESeqResults() object.

gtl
diff --git a/reference/export_to_sif.html b/reference/export_to_sif.html index 6808846..a27e2dd 100644 --- a/reference/export_to_sif.html +++ b/reference/export_to_sif.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -102,7 +102,7 @@

Examples

g <- make_full_graph(5) %du% make_full_graph(5) %du% make_full_graph(5) g <- add_edges(g, c(1, 6, 1, 11, 6, 11)) export_to_sif(g, tempfile()) -#> Saving the file to /var/folders/3s/b36dp_4s3wv3byw057j8bp940000gn/T//RtmpWbnlgS/file11d7867ab4d16 +#> Saving the file to /var/folders/ml/x_tvfgn50_s7p67dm1ypcqqm0000gn/T//RtmpeqSg72/file1184c623346b2 #> Done! diff --git a/reference/fgseaRes.html b/reference/fgseaRes.html index 303a288..f72654e 100644 --- a/reference/fgseaRes.html +++ b/reference/fgseaRes.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gene_plot.html b/reference/gene_plot.html index 2a079d1..da57f4b 100644 --- a/reference/gene_plot.html +++ b/reference/gene_plot.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -75,7 +75,7 @@

Plot expression values for a gene

gene_plot(
   dds,
   gene,
-  intgroup = "condition",
+  intgroup = NULL,
   assay = "counts",
   annotation_obj = NULL,
   normalized = TRUE,
@@ -104,7 +104,8 @@ 
Arguments

 
 
intgroup

 
A character vector of names in colData(dds) to use for grouping.
-Note: the vector components should be categorical variables.

+Note: the vector components should be categorical variables. Defaults
+to NULL, which which would then select the first column of the colData slot.

 
 
 
assay

diff --git a/reference/geneinfo_2_html.html b/reference/geneinfo_2_html.html
index 0baa760..cce1120 100644
--- a/reference/geneinfo_2_html.html
+++ b/reference/geneinfo_2_html.html
@@ -17,7 +17,7 @@
       
       
         GeneTonic
-        3.1.0
+        3.1.1
diff --git a/reference/get_aggrscores.html b/reference/get_aggrscores.html index 200aeb8..8d9bc66 100644 --- a/reference/get_aggrscores.html +++ b/reference/get_aggrscores.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/get_expression_values.html b/reference/get_expression_values.html index f16d1f6..7c1eaab 100644 --- a/reference/get_expression_values.html +++ b/reference/get_expression_values.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/ggs_backbone.html b/reference/ggs_backbone.html index 7695c85..e6cf48e 100644 --- a/reference/ggs_backbone.html +++ b/reference/ggs_backbone.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/ggs_graph.html b/reference/ggs_graph.html index 551ee70..91aa3d7 100644 --- a/reference/ggs_graph.html +++ b/reference/ggs_graph.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -192,10 +192,10 @@

Examples

) ggs -#> IGRAPH 3156d5e UN-- 253 569 -- +#> IGRAPH b79a63b UN-- 253 569 -- #> + attr: name (v/c), nodetype (v/c), shape (v/c), color (v/c), title #> | (v/c) -#> + edges from 3156d5e (vertex names): +#> + edges from b79a63b (vertex names): #> [1] adaptive immune response--B2M adaptive immune response--BCL6 #> [3] adaptive immune response--BTN3A1 adaptive immune response--BTN3A2 #> [5] adaptive immune response--BTN3A3 adaptive immune response--C1QB @@ -205,7 +205,7 @@

Examples

#> [13] adaptive immune response--C4B adaptive immune response--CD1A #> + ... omitted several edges -#' # could be viewed interactively with +# could be viewed interactively with # library(visNetwork) # library(magrittr) # ggs %>% diff --git a/reference/go_2_html.html b/reference/go_2_html.html index 24c157c..0b694f6 100644 --- a/reference/go_2_html.html +++ b/reference/go_2_html.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gostres_macrophage.html b/reference/gostres_macrophage.html index ae61317..5d44d61 100644 --- a/reference/gostres_macrophage.html +++ b/reference/gostres_macrophage.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_alluvial.html b/reference/gs_alluvial.html index 5bcd2e6..5e5f5fd 100644 --- a/reference/gs_alluvial.html +++ b/reference/gs_alluvial.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -178,7 +178,7 @@

Examples

n_gs = 4 )
-# or using the alias... +# or using the alias... gs_sankey( res_enrich = res_enrich, res_de = res_de, @@ -186,7 +186,7 @@

Examples

n_gs = 4 )
- + diff --git a/reference/gs_fuzzyclustering.html b/reference/gs_fuzzyclustering.html index 2bc6e7c..6538883 100644 --- a/reference/gs_fuzzyclustering.html +++ b/reference/gs_fuzzyclustering.html @@ -19,7 +19,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_heatmap.html b/reference/gs_heatmap.html index 4863edd..49e01b6 100644 --- a/reference/gs_heatmap.html +++ b/reference/gs_heatmap.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_horizon.html b/reference/gs_horizon.html index 4dcc5f1..37b5d07 100644 --- a/reference/gs_horizon.html +++ b/reference/gs_horizon.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_mds.html b/reference/gs_mds.html index 28cdf7f..62f48a7 100644 --- a/reference/gs_mds.html +++ b/reference/gs_mds.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_radar.html b/reference/gs_radar.html index 8715f98..c8aa422 100644 --- a/reference/gs_radar.html +++ b/reference/gs_radar.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -162,10 +162,10 @@

Examples

res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) gs_radar(res_enrich = res_enrich)
-# or using the alias... +# or using the alias... gs_spider(res_enrich = res_enrich)
- + # with more than one set res_enrich2 <- res_enrich[1:60, ] set.seed(42) @@ -177,7 +177,7 @@

Examples

res_enrich2 = res_enrich2 )
- + diff --git a/reference/gs_scoresheat.html b/reference/gs_scoresheat.html index b946191..5425456 100644 --- a/reference/gs_scoresheat.html +++ b/reference/gs_scoresheat.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_simplify.html b/reference/gs_simplify.html index d080260..9f8bc4d 100644 --- a/reference/gs_simplify.html +++ b/reference/gs_simplify.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_summary_heat.html b/reference/gs_summary_heat.html index 3d24968..5005ae0 100644 --- a/reference/gs_summary_heat.html +++ b/reference/gs_summary_heat.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_summary_overview.html b/reference/gs_summary_overview.html index a9ec726..e7ed3f6 100644 --- a/reference/gs_summary_overview.html +++ b/reference/gs_summary_overview.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_summary_overview_pair.html b/reference/gs_summary_overview_pair.html index 6b6cde0..04d6063 100644 --- a/reference/gs_summary_overview_pair.html +++ b/reference/gs_summary_overview_pair.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_upset.html b/reference/gs_upset.html index 2c9f8f2..db7448d 100644 --- a/reference/gs_upset.html +++ b/reference/gs_upset.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/gs_volcano.html b/reference/gs_volcano.html index 97e3161..6581c73 100644 --- a/reference/gs_volcano.html +++ b/reference/gs_volcano.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/happy_hour.html b/reference/happy_hour.html index 3ab0ae7..a9e33ed 100644 --- a/reference/happy_hour.html +++ b/reference/happy_hour.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/index.html b/reference/index.html index aa9129e..c6b7ecc 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/map2color.html b/reference/map2color.html index e0b36b0..b20dd15 100644 --- a/reference/map2color.html +++ b/reference/map2color.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -84,7 +84,7 @@

Arguments

pal

A vector of characters specifying the definition of colors for the -palette, e.g. obtained via brewer.pal

+palette, e.g. obtained via RColorBrewer::brewer.pal()

symmetric
diff --git a/reference/overlap_coefficient.html b/reference/overlap_coefficient.html index 4a1460c..8bdae7f 100644 --- a/reference/overlap_coefficient.html +++ b/reference/overlap_coefficient.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/overlap_jaccard_index.html b/reference/overlap_jaccard_index.html index 6c47a98..fb6a78c 100644 --- a/reference/overlap_jaccard_index.html +++ b/reference/overlap_jaccard_index.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/res_macrophage_IFNg_vs_naive.html b/reference/res_macrophage_IFNg_vs_naive.html index 82be102..502cb3e 100644 --- a/reference/res_macrophage_IFNg_vs_naive.html +++ b/reference/res_macrophage_IFNg_vs_naive.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_davidResult.html b/reference/shake_davidResult.html index a97313d..bd1c784 100644 --- a/reference/shake_davidResult.html +++ b/reference/shake_davidResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_enrichResult.html b/reference/shake_enrichResult.html index 1151da9..7eaea47 100644 --- a/reference/shake_enrichResult.html +++ b/reference/shake_enrichResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_enrichrResult.html b/reference/shake_enrichrResult.html index ed998b8..3bec23c 100644 --- a/reference/shake_enrichrResult.html +++ b/reference/shake_enrichrResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_fgseaResult.html b/reference/shake_fgseaResult.html index 50c4a43..c7a92cd 100644 --- a/reference/shake_fgseaResult.html +++ b/reference/shake_fgseaResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_gprofilerResult.html b/reference/shake_gprofilerResult.html index 5b47d1c..eadd2c4 100644 --- a/reference/shake_gprofilerResult.html +++ b/reference/shake_gprofilerResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_gsenrichResult.html b/reference/shake_gsenrichResult.html index 1e6290f..804afe1 100644 --- a/reference/shake_gsenrichResult.html +++ b/reference/shake_gsenrichResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/shake_topGOtableResult.html b/reference/shake_topGOtableResult.html index 0b6d875..e9c5a4f 100644 --- a/reference/shake_topGOtableResult.html +++ b/reference/shake_topGOtableResult.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/signature_volcano.html b/reference/signature_volcano.html index b05aab8..ebb734e 100644 --- a/reference/signature_volcano.html +++ b/reference/signature_volcano.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1 @@ -143,7 +143,7 @@

Arguments

Value

-

A plot returned by the ggplot() function

+

A ggplot object

diff --git a/reference/styleColorBar_divergent.html b/reference/styleColorBar_divergent.html index ddef22c..54be0fc 100644 --- a/reference/styleColorBar_divergent.html +++ b/reference/styleColorBar_divergent.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1
diff --git a/reference/summarize_ggs_hubgenes.html b/reference/summarize_ggs_hubgenes.html index 28e30b1..d31574a 100644 --- a/reference/summarize_ggs_hubgenes.html +++ b/reference/summarize_ggs_hubgenes.html @@ -17,7 +17,7 @@ GeneTonic - 3.1.0 + 3.1.1 diff --git a/reference/topgoDE_macrophage_IFNg_vs_naive.html b/reference/topgoDE_macrophage_IFNg_vs_naive.html index da74d78..bc2695e 100644 --- a/reference/topgoDE_macrophage_IFNg_vs_naive.html +++ b/reference/topgoDE_macrophage_IFNg_vs_naive.html @@ -18,7 +18,7 @@ GeneTonic - 3.1.0 + 3.1.1