Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2024). teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application. -R package version 0.1.5.9011, +R package version 0.1.5.9012, https://github.com/insightsengineering/teal.modules.hermes/, https://insightsengineering.github.io/teal.modules.hermes/.
@Manual{, title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application}, author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang}, year = {2024}, - note = {R package version 0.1.5.9011, + note = {R package version 0.1.5.9012, https://github.com/insightsengineering/teal.modules.hermes/}, url = {https://insightsengineering.github.io/teal.modules.hermes/}, }
assaySpec
adtteSpec
geneSpec
teal_data
reactive(<teal_data>)
teal::init()
data
moduleServer
plot_with_settings_srv
teal.devel
teal::root_modules
teal::modules
geneSpecInput
hermes
ui <- function(id, - data, mae_name) { ns <- NS(id) teal.widgets::standard_layout( - encoding = div( - experimentSpecInput( - ns("my_experiment"), - data, - mae_name, - label_experiments = "Please choose experiment" - ), - selectInput( - ns("property"), - "Please choose property", - c("data", "name", "genes", "assays") - ) - ), + encoding = uiOutput(ns("encoding_ui")), output = div( verbatimTextOutput(ns("summary")), verbatimTextOutput(ns("head")) @@ -159,6 +137,21 @@ Examples filter_panel_api, mae_name) { moduleServer(id, function(input, output, session) { + output$encoding_ui <- renderUI({ + div( + experimentSpecInput( + session$ns("my_experiment"), + data, + mae_name, + label_experiments = "Please choose experiment" + ), + selectInput( + session$ns("property"), + "Please choose property", + c("data", "name", "genes", "assays") + ) + ) + }) experiment <- experimentSpecServer( "my_experiment", data, @@ -166,6 +159,7 @@ Examples mae_name ) result <- reactive({ + req(input$property) switch(input$property, data = experiment$data(), name = experiment$name(), diff --git a/main/reference/function_arguments.html b/main/reference/function_arguments.html index 705bce51..7a3fbc8c 100644 --- a/main/reference/function_arguments.html +++ b/main/reference/function_arguments.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/geneSpecInput.html b/main/reference/geneSpecInput.html index 875759a7..6ccd252f 100644 --- a/main/reference/geneSpecInput.html +++ b/main/reference/geneSpecInput.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/geneSpecServer.html b/main/reference/geneSpecServer.html index 0aad7517..fa1f5c1d 100644 --- a/main/reference/geneSpecServer.html +++ b/main/reference/geneSpecServer.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_assign_to_group_list.html b/main/reference/h_assign_to_group_list.html index 31e5332a..9313d611 100644 --- a/main/reference/h_assign_to_group_list.html +++ b/main/reference/h_assign_to_group_list.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_collapse_levels.html b/main/reference/h_collapse_levels.html index 66cf6fe2..dc4c5b63 100644 --- a/main/reference/h_collapse_levels.html +++ b/main/reference/h_collapse_levels.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_extract_words.html b/main/reference/h_extract_words.html index 03ac7a8e..38ad3030 100644 --- a/main/reference/h_extract_words.html +++ b/main/reference/h_extract_words.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_gene_data.html b/main/reference/h_gene_data.html index eb1402d1..dd859144 100644 --- a/main/reference/h_gene_data.html +++ b/main/reference/h_gene_data.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_km_mae_to_adtte.html b/main/reference/h_km_mae_to_adtte.html index 33026c76..f9b3b460 100644 --- a/main/reference/h_km_mae_to_adtte.html +++ b/main/reference/h_km_mae_to_adtte.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_order_genes.html b/main/reference/h_order_genes.html index e0df8fb3..b0469b99 100644 --- a/main/reference/h_order_genes.html +++ b/main/reference/h_order_genes.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_parse_genes.html b/main/reference/h_parse_genes.html index 4beee31b..54f168e1 100644 --- a/main/reference/h_parse_genes.html +++ b/main/reference/h_parse_genes.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/h_update_gene_selection.html b/main/reference/h_update_gene_selection.html index 4aee24aa..e6f6649d 100644 --- a/main/reference/h_update_gene_selection.html +++ b/main/reference/h_update_gene_selection.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/heatmap_plot.html b/main/reference/heatmap_plot.html index 1ff97744..c589a629 100644 --- a/main/reference/heatmap_plot.html +++ b/main/reference/heatmap_plot.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/include_css_files.html b/main/reference/include_css_files.html index c0e5c56a..86152676 100644 --- a/main/reference/include_css_files.html +++ b/main/reference/include_css_files.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/include_js_files.html b/main/reference/include_js_files.html index 4b1df006..c97cff6d 100644 --- a/main/reference/include_js_files.html +++ b/main/reference/include_js_files.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/index.html b/main/reference/index.html index d291151c..3ef8a57c 100644 --- a/main/reference/index.html +++ b/main/reference/index.html @@ -10,7 +10,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -27,15 +27,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/is_blank.html b/main/reference/is_blank.html index 2f26a301..ca8b392f 100644 --- a/main/reference/is_blank.html +++ b/main/reference/is_blank.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/module_arguments.html b/main/reference/module_arguments.html index 0fd1d083..8bc57c3e 100644 --- a/main/reference/module_arguments.html +++ b/main/reference/module_arguments.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/multiSampleVarSpecServer.html b/main/reference/multiSampleVarSpecServer.html index c2c94ba5..11779562 100644 --- a/main/reference/multiSampleVarSpecServer.html +++ b/main/reference/multiSampleVarSpecServer.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/rADTTE.html b/main/reference/rADTTE.html index ac5addcc..6087a659 100644 --- a/main/reference/rADTTE.html +++ b/main/reference/rADTTE.html @@ -10,7 +10,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -27,15 +27,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/sampleVarSpecInput.html b/main/reference/sampleVarSpecInput.html index 969e7698..fc36bf05 100644 --- a/main/reference/sampleVarSpecInput.html +++ b/main/reference/sampleVarSpecInput.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/sampleVarSpecServer.html b/main/reference/sampleVarSpecServer.html index a3a46723..7021b1a3 100644 --- a/main/reference/sampleVarSpecServer.html +++ b/main/reference/sampleVarSpecServer.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/teal.modules.hermes-package.html b/main/reference/teal.modules.hermes-package.html index 10a77420..0719779e 100644 --- a/main/reference/teal.modules.hermes-package.html +++ b/main/reference/teal.modules.hermes-package.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/tm_g_barplot.html b/main/reference/tm_g_barplot.html index 3e377956..b0514fe4 100644 --- a/main/reference/tm_g_barplot.html +++ b/main/reference/tm_g_barplot.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -171,7 +162,7 @@ Examples ) ) ) -#> [INFO] 2024-02-09 12:20:05.4133 pid:1221 token:[] teal.modules.hermes Initializing tm_g_barplot +#> [INFO] 2024-02-13 15:41:36.6630 pid:1221 token:[] teal.modules.hermes Initializing tm_g_barplot if (interactive()) { shinyApp(app$ui, app$server) } diff --git a/main/reference/tm_g_boxplot.html b/main/reference/tm_g_boxplot.html index 1906cb77..9d53d423 100644 --- a/main/reference/tm_g_boxplot.html +++ b/main/reference/tm_g_boxplot.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -171,7 +162,7 @@ Examples ) ) ) -#> [INFO] 2024-02-09 12:20:05.7433 pid:1221 token:[] teal.modules.hermes Initializing tm_g_boxplot +#> [INFO] 2024-02-13 15:41:36.9907 pid:1221 token:[] teal.modules.hermes Initializing tm_g_boxplot if (interactive()) { shinyApp(app$ui, app$server) } diff --git a/main/reference/tm_g_forest_tte.html b/main/reference/tm_g_forest_tte.html index 0767acb0..542b7c0b 100644 --- a/main/reference/tm_g_forest_tte.html +++ b/main/reference/tm_g_forest_tte.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -222,7 +213,7 @@ Examples ) ) ) -#> [INFO] 2024-02-09 12:20:06.0515 pid:1221 token:[] teal.modules.hermes Initializing tm_g_forest_tte +#> [INFO] 2024-02-13 15:41:37.2944 pid:1221 token:[] teal.modules.hermes Initializing tm_g_forest_tte if (interactive()) { shinyApp(app$ui, app$server) } diff --git a/main/reference/tm_g_km.html b/main/reference/tm_g_km.html index 03c2c140..20a260c6 100644 --- a/main/reference/tm_g_km.html +++ b/main/reference/tm_g_km.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -202,7 +193,7 @@ Examples mae_name = "MAE" ) ) -#> [INFO] 2024-02-09 12:20:06.5699 pid:1221 token:[] teal.modules.hermes Initializing tm_g_km +#> [INFO] 2024-02-13 15:41:37.9011 pid:1221 token:[] teal.modules.hermes Initializing tm_g_km app <- init( data = data, diff --git a/main/reference/tm_g_pca.html b/main/reference/tm_g_pca.html index 30aa1afb..74f4e0d9 100644 --- a/main/reference/tm_g_pca.html +++ b/main/reference/tm_g_pca.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -158,7 +149,7 @@ Examples ) ) ) -#> [INFO] 2024-02-09 12:20:06.9201 pid:1221 token:[] teal.modules.hermes Initializing tm_g_pca +#> [INFO] 2024-02-13 15:41:38.2491 pid:1221 token:[] teal.modules.hermes Initializing tm_g_pca if (interactive()) { shinyApp(app$ui, app$server) } diff --git a/main/reference/tm_g_quality.html b/main/reference/tm_g_quality.html index 032c4890..05599f8b 100644 --- a/main/reference/tm_g_quality.html +++ b/main/reference/tm_g_quality.html @@ -16,7 +16,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -33,15 +33,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/tm_g_scatterplot.html b/main/reference/tm_g_scatterplot.html index 11d9589f..44cfbe7f 100644 --- a/main/reference/tm_g_scatterplot.html +++ b/main/reference/tm_g_scatterplot.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -171,7 +162,7 @@ Examples ) ) ) -#> [INFO] 2024-02-09 12:20:07.4803 pid:1221 token:[] teal.modules.hermes Initializing tm_g_scatterplot +#> [INFO] 2024-02-13 15:41:38.8073 pid:1221 token:[] teal.modules.hermes Initializing tm_g_scatterplot if (interactive()) { shinyApp(app$ui, app$server) } diff --git a/main/reference/tm_g_volcanoplot.html b/main/reference/tm_g_volcanoplot.html index 97278e1c..a8ccb533 100644 --- a/main/reference/tm_g_volcanoplot.html +++ b/main/reference/tm_g_volcanoplot.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - @@ -162,7 +153,7 @@ Examples ) ) ) -#> [INFO] 2024-02-09 12:20:07.7707 pid:1221 token:[] teal.modules.hermes Initializing tm_g_volcanoplot +#> [INFO] 2024-02-13 15:41:39.0984 pid:1221 token:[] teal.modules.hermes Initializing tm_g_volcanoplot if (interactive()) { shinyApp(app$ui, app$server) } diff --git a/main/reference/top_gene_plot.html b/main/reference/top_gene_plot.html index 6669ccd3..df1dd173 100644 --- a/main/reference/top_gene_plot.html +++ b/main/reference/top_gene_plot.html @@ -12,7 +12,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -29,15 +29,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/validate_gene_spec.html b/main/reference/validate_gene_spec.html index 4e5b7b7c..1a7f676e 100644 --- a/main/reference/validate_gene_spec.html +++ b/main/reference/validate_gene_spec.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/reference/validate_n_levels.html b/main/reference/validate_n_levels.html index 9b478d62..5c2b3c1d 100644 --- a/main/reference/validate_n_levels.html +++ b/main/reference/validate_n_levels.html @@ -14,7 +14,7 @@ teal.modules.hermes - 0.1.5.9011 + 0.1.5.9012 part of @@ -31,15 +31,6 @@ Changelog - - Versions main -latest-tag -v0.1.5 -v0.1.4 - diff --git a/main/search.json b/main/search.json index c63edfd1..89c40505 100644 --- a/main/search.json +++ b/main/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: _. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: __. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started","text":"teal.modules.hermes package implementing number teal modules exploration RNA-sequencing counts data. addition predefined modules, teal.modules.hermes enables quick easy ad-hoc module creation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"ad-hoc-module-example","dir":"Articles","previous_headings":"","what":"Ad-hoc module example","title":"Getting Started","text":"Let’s assume function awesome_plot() takes count matrix makes awesome plot . Now like make Shiny app can filter patients, samples, select experiment MultiAssayExperiment (MAE), select count matrix experiment, etc. Nothing easier teal.modules.hermes! show quickly spin UI, server put together nice little app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"ui-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"UI function","title":"Getting Started","text":"teal.modules.hermes provide modules make experiment assay selection super easy, see UI part:","code":"ui <- function(id, mae_name) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = plotOutput(ns(\"awesome_plot\")) ) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"server-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Server function","title":"Getting Started","text":"Similarly server use modules, call awesome plotting function.","code":"srv <- function(input, output, session, data, filter_panel_api, mae_name) { output$encoding_ui <- renderUI({ div( experimentSpecInput(session$ns(\"experiment\"), data, mae_name), assaySpecInput(session$ns(\"assay\")) ) }) experiment <- experimentSpecServer( \"experiment\", data = data, filter_panel_api = filter_panel_api, mae_name = mae_name, name_annotation = NULL # If you have a gene name column in your rowData, can specify here. ) assay <- assaySpecServer(\"assay\", experiment$assays) output$awesome_plot <- renderPlot({ data <- experiment$data() assay <- assay() req(assay %in% SummarizedExperiment::assayNames(data)) counts <- SummarizedExperiment::assay(data, assay) df <- data.frame(gene = rownames(counts), counts = rowSums(counts)) df <- na.omit(df[order(df$counts, decreasing = TRUE), ]) df$gene <- factor(df$gene, levels = df$gene) df <- df[1:10, ] ggplot(df, aes(x = gene, y = counts)) + geom_col() + theme(axis.text.x = element_text(angle = 90)) }) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"app-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"App function","title":"Getting Started","text":"Now let’s assume want spin app MAE.","code":"awesome_app <- function(mae, label = \"My awesome app\") { mae_name <- \"MAE\" data <- teal_data(MAE = hermes::lapply(mae, hermes::HermesData)) app <- init( data = data, modules = teal::modules( module( label = label, server = srv, server_args = list(mae_name = mae_name), ui = ui, ui_args = list(mae_name = mae_name), datanames = mae_name ) ) ) shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"testing-it","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Testing it","title":"Getting Started","text":"test :","code":"awesome_app(hermes::multi_assay_experiment)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Nikolas Burkoff. Author. Dinakar Kulkarni. Author. Konrad Pagacz. Author. Namrata Bhatia. Author. Dawid Kaledkowski. Author. Pawel Rucki. Author. Jeff Luong. Author. Stefanie Bienert. Author. Haocheng Li. Author. Lyndsee Midori Zhang. Author. Sorin Voicu. Contributor. Benoit Falquet. Contributor. Mahmoud Hallal. Contributor. Tim Treis. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2024). teal.modules.hermes: RNA-Seq Analysis Modules Add Teal Application. R package version 0.1.5.9011, https://github.com/insightsengineering/teal.modules.hermes/, https://insightsengineering.github.io/teal.modules.hermes/main/.","code":"@Manual{, title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application}, author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang}, year = {2024}, note = {R package version 0.1.5.9011, https://github.com/insightsengineering/teal.modules.hermes/}, url = {https://insightsengineering.github.io/teal.modules.hermes/main/}, }"},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"what-is-teal","dir":"","previous_headings":"What is what","what":"What is teal?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal shiny-based interactive exploration framework analyzing clinical trials data. teal currently provides dynamic filtering facility diverse data viewers. teal shiny applications built using standard shiny modules. See teal page details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"what-is-hermes","dir":"","previous_headings":"What is what","what":"What is hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data. core functionality built BioConductor ecosystem, especially SummarizedExperiment class HermesData class inherits. See vignette details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"so-what-is-then-tealmoduleshermes","dir":"","previous_headings":"What is what","what":"So what is then teal.modules.hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal.modules.hermes provides teal modules (can used part teal app), interactive RNA-seq data analysis using hermes. heavily built BioConductor classes, particular MultiAssayExperiment (MAE) expected contain HermesData experiments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"July 2023 insightsengineering packages available r-universe. See package vignettes browseVignettes(package = \"teal.modules.hermes\") usage package.","code":"# stable versions install.packages('teal.modules.hermes', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org')) # beta versions install.packages('teal.modules.hermes', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/pull_request_template.html","id":null,"dir":"","previous_headings":"","what":"Pull Request","title":"Pull Request","text":"Fixes #nnn","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for ADTTE Specification — adtteSpecInput","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"defines input ADTTE specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"","code":"adtteSpecInput(inputId, label_paramcd = \"Select Endpoint\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"inputId (string) ID used call module input. label_paramcd (string) label endpoint (PARAMCD) selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for ADTTE Specification — adtteSpecServer","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"defines server part ADTTE specification. resulting data set binned_adtte_subset contains subset ADTTE selected time--event endpoint, joined together gene information extracted specified assay experiment, numeric factor columns. factor column created binning numeric column according quantile cutoffs specified probs.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"adtteSpecServer( id, data, mae_name, adtte_name, adtte_vars, experiment_data, experiment_name, assay, genes, probs )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"id (string) shiny module id. data (reactive)reactive() holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. experiment_data (reactive AnyHermesData) input experiment. experiment_name (reactive string) name input experiment. assay (reactive string) name assay. genes (reactive GeneSpec) gene specification. probs (reactive numeric) probabilities bin gene gene signature .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"List following elements: binned_adtte_subset: reactive containing joined ADTTE gene data. gene_col: reactive containing string column name original numeric gene variable. gene_factor: string variable name binned gene data. time_unit: reactive string time unit current subset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"ui <- function(id) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = verbatimTextOutput(ns(\"summary\")) ) } server <- function(id, data, filter_panel_api) { checkmate::assert_class(data, \"reactive\") checkmate::assert_class(shiny::isolate(data()), \"teal_data\") moduleServer(id, function(input, output, session) { output$encoding_ui <- renderUI({ div( experimentSpecInput(session$ns(\"experiment\"), data, mae_name = \"MAE\"), assaySpecInput(session$ns(\"assay\")), geneSpecInput(session$ns(\"genes\"), funs = list(Mean = colMeans)), adtteSpecInput(session$ns(\"adtte\")) ) }) experiment <- experimentSpecServer( \"experiment\", data = data, filter_panel_api = filter_panel_api, mae_name = \"MAE\" ) assay <- assaySpecServer( \"assay\", assays = experiment$assays ) genes <- geneSpecServer( \"genes\", funs = list(Mean = colMeans), gene_choices = experiment$genes ) adtte <- adtteSpecServer( \"adtte\", data = data, adtte_name = \"ADTTE\", mae_name = \"MAE\", adtte_vars = list( aval = \"AVAL\", avalu = \"AVALU\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid = \"USUBJID\" ), experiment_data = experiment$data, experiment_name = experiment$name, assay = assay, genes = genes, probs = reactive({ 0.5 }) ) output$summary <- renderPrint({ binned_adtte_subset <- adtte$binned_adtte_subset() summary(binned_adtte_subset) }) }) } my_app <- function() { data <- teal_data() data <- within(data, { ADSL <- teal.data::rADSL ADTTE <- teal.modules.hermes::rADTTE %>% dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( module( label = \"adtteSpec example\", server = server, ui = ui, datanames = \"all\" ) ) ) shinyApp(app$ui, app$server) } if (interactive()) { my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Assay Specification — assaySpecInput","title":"Module Input for Assay Specification — assaySpecInput","text":"defines input assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Assay Specification — assaySpecInput","text":"","code":"assaySpecInput(inputId, label_assays = \"Select Assay\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Assay Specification — assaySpecInput","text":"inputId (string) ID used call module input. label_assays (string) label assay selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Assay Specification — assaySpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Assay Specification — assaySpecServer","title":"Module Server for Assay Specification — assaySpecServer","text":"defines server part assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"assaySpecServer(id, assays, exclude_assays = character())"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Assay Specification — assaySpecServer","text":"id (string) shiny module id. assays (reactive character) available assays currently selected experiment. exclude_assays (character) names assays included choices teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Assay Specification — assaySpecServer","text":"chosen assay reactive string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"ui <- function(id) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = textOutput(ns(\"result\")) ) } server <- function(id, data, filter_panel_api) { moduleServer(id, module = function(input, output, session) { output$encoding_ui <- renderUI({ div( experimentSpecInput(session$ns(\"experiment\"), data, \"MAE\"), assaySpecInput( session$ns(\"assay\"), label_assays = \"Please choose assay\" ) ) }) experiment <- experimentSpecServer( id = \"experiment\", data = data, filter_panel_api = filter_panel_api, mae_name = \"MAE\" ) assay <- assaySpecServer( \"assay\", experiment$assays, exclude_assays = c(\"counts\", \"cpm\", \"tpm\", \"bla\") ) output$result <- renderPrint({ assay() }) }) } my_app <- function() { data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init( data = data, modules = modules( module( label = \"assaySpec example\", server = server, ui = ui, datanames = \"all\" ) ) ) shinyApp(app$ui, app$server) } if (interactive()) { my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for ADTTE Variables — assert_adtte_vars","title":"Check for ADTTE Variables — assert_adtte_vars","text":"Check whether x list ADTTE variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for ADTTE Variables — assert_adtte_vars","text":"x object check.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(list(aval = \"AV\", is_event = \"EV\", paramcd = \"PC\", usubjid = \"ID\", avalu = \"u\"))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for List of Summary Functions — assert_summary_funs","title":"Check for List of Summary Functions — assert_summary_funs","text":"Check whether x list summary functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(x, null.ok = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for List of Summary Functions — assert_summary_funs","text":"x object check. null.ok (flag) whether x may also contain NULL, meaning user choice possible summary function applied.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertion_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Assertion Arguments — assertion_arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"documentation function lists conventional arguments additional checkmate assertions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertion_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for checkmate — assertions","title":"Additional Assertions for checkmate — assertions","text":"provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for checkmate — assertions","text":"Depending function prefix. assert_ functions return object invisibly successful, otherwise throw error message. check_ functions return TRUE successful, otherwise string error message. test_ functions just return TRUE FALSE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Reactive Input — check_reactive","title":"Check for Reactive Input — check_reactive","text":"Check whether x reactive input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(x) assert_reactive(x, .var.name = checkmate::vname(x), add = NULL) test_reactive(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Reactive Input — check_reactive","text":"x object check. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(\"bla\") #> [1] FALSE check_reactive(reactive(\"bla\")) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Shiny Tag — check_tag","title":"Check for Shiny Tag — check_tag","text":"Check whether x shiny tag.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(x, null.ok = FALSE) assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL) test_tag(x, null.ok = FALSE) expect_tag(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Shiny Tag — check_tag","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(\"bla\") #> [1] \"Must be a 'shiny.tag' or NULL\" check_tag(NULL, null.ok = TRUE) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Experiment Specification — experimentSpecInput","title":"Module Input for Experiment Specification — experimentSpecInput","text":"defines input experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Experiment Specification — experimentSpecInput","text":"","code":"experimentSpecInput( inputId, data, mae_name, label_experiments = \"Select Experiment\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Experiment Specification — experimentSpecInput","text":"inputId (string) ID used call module input. data (reactive)reactive() holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. label_experiments (string) label experiment selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Experiment Specification — experimentSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Experiment Specification — experimentSpecServer","title":"Module Server for Experiment Specification — experimentSpecServer","text":"defines server part experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"experimentSpecServer( id, data, filter_panel_api, mae_name, name_annotation = \"symbol\", sample_vars_as_factors = TRUE, with_mae_col_data = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Experiment Specification — experimentSpecServer","text":"id (string) shiny module id. data (reactive)reactive() holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. mae_name (string) name MAE data used teal module. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings. sample_vars_as_factors (flag) whether convert sample variables (columns colData() experiment) character factor variables. with_mae_col_data (flag) whether include colData() MAE experiment colData().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Experiment Specification — experimentSpecServer","text":"List following reactive objects: data: hermes::AnyHermesData experiment. name: name experiment selected user. genes: data.frame genes data, columns id name. assays: names assays data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"ui <- function(id, data, mae_name) { ns <- NS(id) teal.widgets::standard_layout( encoding = div( experimentSpecInput( ns(\"my_experiment\"), data, mae_name, label_experiments = \"Please choose experiment\" ), selectInput( ns(\"property\"), \"Please choose property\", c(\"data\", \"name\", \"genes\", \"assays\") ) ), output = div( verbatimTextOutput(ns(\"summary\")), verbatimTextOutput(ns(\"head\")) ) ) } server <- function(id, data, filter_panel_api, mae_name) { moduleServer(id, function(input, output, session) { experiment <- experimentSpecServer( \"my_experiment\", data, filter_panel_api, mae_name ) result <- reactive({ switch(input$property, data = experiment$data(), name = experiment$name(), genes = experiment$genes(), assays = experiment$assays() ) }) output$summary <- renderPrint({ result <- result() hermes::summary(result) }) output$head <- renderPrint({ result <- result() utils::head(result) }) }) } my_app <- function() { data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init( data = data, modules = modules( module( label = \"experimentSpec example\", server = server, server_args = list(mae_name = \"MAE\"), ui = ui, ui_args = list(mae_name = \"MAE\"), datanames = \"all\" ) ) ) shinyApp(app$ui, app$server) } if (interactive()) { my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/function_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Function Arguments — function_arguments","title":"Standard Function Arguments — function_arguments","text":"documentation function lists conventional arguments functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/function_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Function Arguments — function_arguments","text":"adtte (data frame) adtte dataset. usubjid_var (string) variable name subject ID variable. mae (MultiAssayExperiment) contains AnyHermesData objects. object (AnyHermesData) contains RNA-seq values one experiment. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Gene Signature Specification — geneSpecInput","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"defines input gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput( inputId, funs, label_genes = \"Select Gene(s)\", label_funs = \"Select Gene Summary\", label_text_button = \"Enter list of genes\", label_lock_button = \"Lock gene selection (so that it does not get updated when filtering)\", label_select_all_button = paste0(\"Select All Genes (first \", max_options, \")\"), label_select_none_button = \"Select None\", max_options = 200L, max_selected = max_options )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"inputId (string) ID used call module input. funs (named list) names list used function selection drop menu. label_genes (string) label gene selection. label_funs (string) label function selection. label_text_button (string) label text input button. label_lock_button (string) label lock button. label_select_all_button (string) label selecting genes button. label_select_none_button (string) label selecting genes button. max_options (count) maximum number gene options rendering selected via \"Select \". max_selected (count) maximum number genes can selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(\"my_genes\", list(mean = colMeans), label_funs = \"Please select function\") #> #> #> Select Gene(s)<\/label> #> <\/div> #> #> #> #> <\/i> #> <\/span> #> <\/button> #> #> #> <\/i> #> <\/span> #> <\/button> #> <\/div> #> #> #> #> <\/i> #> <\/span> #> <\/button> #> #> #> #> #> #> <\/i> #> #> <\/span> #> <\/label> #> <\/div> #> #> <\/i> #> #> <\/span> #> <\/label> #> <\/div> #> <\/div> #> <\/div> #> <\/div> #> <\/div> #> <\/div> #> #> #> <\/label> #> #> <\/option><\/select> #>
