diff --git a/R/mod_help.R b/R/mod_help.R index 8020916..8804886 100644 --- a/R/mod_help.R +++ b/R/mod_help.R @@ -7,156 +7,459 @@ #' @noRd #' #' @importFrom shiny NS tagList includeMarkdown -mod_help_ui <- function(id){ - ns <- NS(id) +mod_help_ui <- function(id) { tagList( fluidPage( - column(width=12), - column(width=12, - box(title="Convert to VCF", id = "DArT_Report2VCF_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "This tab converts the processed genotype and counts files from DArT into a VCF file (v4.3). This file can then be used as the genotype input for the analyses within BIGapp or used with other genomics applications.", - br(), br(), - bs4Dash::tabsetPanel(id = "DArT_Report2VCF_tabset", - tabPanel("Parameters description", value = "DArT_Report2VCF_par", br(), - includeMarkdown(system.file("help_files/DArT_Report2VCF_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "DArT_Report2VCF_results", br(), - includeMarkdown(system.file("help_files/DArT_Report2VCF_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "DArT_Report2VCF_cite", br(), - includeMarkdown(system.file("help_files/DArT_Report2VCF_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="Dosage Calling", id = "Updog_Dosage_Calling_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "This tab is designed to handle the process of dosage calling in genomic data. Dosage calling is essential for determining the number of copies of a particular allele at each genomic location.", - br(), br(), - bs4Dash::tabsetPanel(id = "Updog_Dosage_Calling_tabset", - tabPanel("Parameters description", value = "Updog_Dosage_Calling_par", br(), - includeMarkdown(system.file("help_files/Updog_Dosage_Calling_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "Updog_Dosage_Calling_results", br(), - includeMarkdown(system.file("help_files/Updog_Dosage_Calling_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "Updog_Dosage_Calling_cite", br(), - includeMarkdown(system.file("help_files/Updog_Dosage_Calling_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="VCF Filtering", id = "VCF_Filtering_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "Filter SNPs and samples in a VCF file based on missing data, minor allele frequency, read depth, and Updog dosage calling metrics", - br(), br(), - bs4Dash::tabsetPanel(id = "VCF_Filtering_tabset", - tabPanel("Parameters description", value = "VCF_Filtering_par", br(), - includeMarkdown(system.file("help_files/VCF_Filtering_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "VCF_Filtering_results", br(), - includeMarkdown(system.file("help_files/VCF_Filtering_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "VCF_Filtering_cite", br(), - includeMarkdown(system.file("help_files/VCF_Filtering_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="PCA", id = "PCA_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "This tab is used to perform a PCA to visualize the genomic relationships between samples (population structure)", - br(), br(), - bs4Dash::tabsetPanel(id = "PCA_tabset", - tabPanel("Parameters description", value = "PCA_par", br(), - includeMarkdown(system.file("help_files/PCA_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "PCA_results", br(), - includeMarkdown(system.file("help_files/PCA_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "PCA_cite", br(), - includeMarkdown(system.file("help_files/PCA_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="DAPC", id = "DAPC_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "This tab group estimates the number of distinct groups that are present within the genomic dataset, and classifies each sample into a distinct group.", - br(), br(), - bs4Dash::tabsetPanel(id = "DAPC_tabset", - tabPanel("Parameters description", value = "DAPC_par", br(), - includeMarkdown(system.file("help_files/DAPC_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "DAPC_results", br(), - includeMarkdown(system.file("help_files/DAPC_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "DAPC_cite", br(), - includeMarkdown(system.file("help_files/DAPC_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="Genomic Diversity", id = "Genomic_Diversity_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "This tab estimates summary metrics for the samples and SNPs within a genomic dataset and produces figures and tables.", - br(), br(), - bs4Dash::tabsetPanel(id = "Genomic_Diversity_tabset", - tabPanel("Parameters description", value = "Genomic_Diversity_par", br(), - includeMarkdown(system.file("help_files/Genomic_Diversity_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "Genomic_Diversity_results", br(), - includeMarkdown(system.file("help_files/Genomic_Diversity_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "Genomic_Diversity_cite", br(), - includeMarkdown(system.file("help_files/Genomic_Diversity_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="GWAS", id = "GWAS_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "The tab is for conducting Genome-Wide Association Studies (GWAS) to identify associations between genetic variants and traits of interest. Users can input phenotypic data and specify parameters for the GWAS analysis. The app performs statistical tests to identify significant associations between SNPs and traits, and visualizes the results using Manhattan plots and Q-Q plots. The tab helps in identifying potential genetic markers linked to specific traits. GWASpoly package is used to perform the analysis.", - br(), br(), - bs4Dash::tabsetPanel(id = "GWAS_tabset", - tabPanel("Parameters description", value = "GWAS_par", br(), - includeMarkdown(system.file("help_files/GWAS_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "GWAS_results", br(), - includeMarkdown(system.file("help_files/GWAS_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "GWAS_cite", br(), - includeMarkdown(system.file("help_files/GWAS_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="Predictive Ability", id = "Predictive_Ability_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "This tab provides the predictive ability of a GBLUP model for each trait across all samples within a genomic dataset", - br(), br(), - bs4Dash::tabsetPanel(id = "Predictive_Ability_tabset", - tabPanel("Parameters description", value = "Predictive_Ability_par", br(), - includeMarkdown(system.file("help_files/Predictive_Ability_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "Predictive_Ability_results", br(), - includeMarkdown(system.file("help_files/Predictive_Ability_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "Predictive_Ability_cite", br(), - includeMarkdown(system.file("help_files/Predictive_Ability_cite.Rmd", package = "BIGapp")) - )) - ), - box(title="Genomic Prediction", id = "Genomic_Prediction_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, - "his tab estimates the trait and estimated-breeding-values (EBVs) for either all individuals in a genomic dataset, or by training the model with one genomic dataset to predict the values in another.", - br(), br(), - bs4Dash::tabsetPanel(id = "Genomic_Prediction_tabset", - tabPanel("Parameters description", value = "Genomic_Prediction_par", br(), - includeMarkdown(system.file("help_files/Genomic_Prediction_par.Rmd", package = "BIGapp")) - ), - tabPanel("Results description", value = "Genomic_Prediction_results", br(), - includeMarkdown(system.file("help_files/Genomic_Prediction_res.Rmd", package = "BIGapp")) - ), - tabPanel("How to cite", value = "Genomic_Prediction_cite", br(), - includeMarkdown(system.file("help_files/Genomic_Prediction_cite.Rmd", package = "BIGapp")) - )) - ), + column( + width = 12, + box( + title = "Convert to VCF", + id = "DArT_Report2VCF_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab converts the processed genotype and counts files from ", + "DArT into a VCF file (v4.3). This file can then be used as the ", + "genotype input for the analyses within BIGapp or used with ", + "other genomics applications." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "DArT_Report2VCF_tabset", + tabPanel( + "Parameters description", + value = "DArT_Report2VCF_par", + br(), + includeMarkdown( + system.file( + "help_files/DArT_Report2VCF_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "DArT_Report2VCF_results", + br(), + includeMarkdown( + system.file( + "help_files/DArT_Report2VCF_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "DArT_Report2VCF_cite", + br(), + includeMarkdown( + system.file( + "help_files/DArT_Report2VCF_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "Dosage Calling", + id = "Updog_Dosage_Calling_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab is designed to handle the process of dosage calling ", + "in genomic data. Dosage calling is essential for determining ", + "the number of copies of a particular allele at each genomic ", + "location." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "Updog_Dosage_Calling_tabset", + tabPanel( + "Parameters description", + value = "Updog_Dosage_Calling_par", + br(), + includeMarkdown( + system.file( + "help_files/Updog_Dosage_Calling_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "Updog_Dosage_Calling_results", + br(), + includeMarkdown( + system.file( + "help_files/Updog_Dosage_Calling_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "Updog_Dosage_Calling_cite", + br(), + includeMarkdown( + system.file( + "help_files/Updog_Dosage_Calling_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "VCF Filtering", + id = "VCF_Filtering_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "Filter SNPs and samples in a VCF file based on missing data, ", + "minor allele frequency, read depth, and Updog dosage calling ", + "metrics." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "VCF_Filtering_tabset", + tabPanel( + "Parameters description", + value = "VCF_Filtering_par", + br(), + includeMarkdown( + system.file( + "help_files/VCF_Filtering_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "VCF_Filtering_results", + br(), + includeMarkdown( + system.file( + "help_files/VCF_Filtering_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "VCF_Filtering_cite", + br(), + includeMarkdown( + system.file( + "help_files/VCF_Filtering_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "PCA", + id = "PCA_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab is used to perform a PCA to visualize the genomic ", + "relationships between samples (population structure)." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "PCA_tabset", + tabPanel( + "Parameters description", + value = "PCA_par", + br(), + includeMarkdown( + system.file( + "help_files/PCA_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "PCA_results", + br(), + includeMarkdown( + system.file( + "help_files/PCA_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "PCA_cite", + br(), + includeMarkdown( + system.file( + "help_files/PCA_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "DAPC", + id = "DAPC_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab group estimates the number of distinct groups that are ", + "present within the genomic dataset and classifies each sample ", + "into a distinct group." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "DAPC_tabset", + tabPanel( + "Parameters description", + value = "DAPC_par", + br(), + includeMarkdown( + system.file( + "help_files/DAPC_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "DAPC_results", + br(), + includeMarkdown( + system.file( + "help_files/DAPC_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "DAPC_cite", + br(), + includeMarkdown( + system.file( + "help_files/DAPC_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "Genomic Diversity", + id = "Genomic_Diversity_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab estimates summary metrics for the samples and SNPs ", + "within a genomic dataset and produces figures and tables." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "Genomic_Diversity_tabset", + tabPanel( + "Parameters description", + value = "Genomic_Diversity_par", + br(), + includeMarkdown( + system.file( + "help_files/Genomic_Diversity_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "Genomic_Diversity_results", + br(), + includeMarkdown( + system.file( + "help_files/Genomic_Diversity_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "Genomic_Diversity_cite", + br(), + includeMarkdown( + system.file( + "help_files/Genomic_Diversity_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "GWAS", + id = "GWAS_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab is for conducting Genome-Wide Association Studies ", + "(GWAS) to identify associations between genetic variants and ", + "traits of interest. Users can input phenotypic data and specify ", + "parameters for the GWAS analysis. The app performs statistical ", + "tests to identify significant associations between SNPs and ", + "traits and visualizes the results using Manhattan plots and Q-Q ", + "plots. The tab helps in identifying potential genetic markers ", + "linked to specific traits. GWASpoly package is used to perform ", + "the analysis." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "GWAS_tabset", + tabPanel( + "Parameters description", + value = "GWAS_par", + br(), + includeMarkdown( + system.file( + "help_files/GWAS_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "GWAS_results", + br(), + includeMarkdown( + system.file( + "help_files/GWAS_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "GWAS_cite", + br(), + includeMarkdown( + system.file( + "help_files/GWAS_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "Predictive Ability", + id = "Predictive_Ability_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab provides the predictive ability of a GBLUP model for ", + "each trait across all samples within a genomic dataset." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "Predictive_Ability_tabset", + tabPanel( + "Parameters description", + value = "Predictive_Ability_par", + br(), + includeMarkdown( + system.file( + "help_files/Predictive_Ability_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "Predictive_Ability_results", + br(), + includeMarkdown( + system.file( + "help_files/Predictive_Ability_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "Predictive_Ability_cite", + br(), + includeMarkdown( + system.file( + "help_files/Predictive_Ability_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), + box( + title = "Genomic Prediction", + id = "Genomic_Prediction_box", + width = 12, + collapsible = TRUE, + collapsed = TRUE, + status = "info", + solidHeader = TRUE, + # content + paste0( + "This tab estimates the trait and estimated-breeding-values ", + "(EBVs) for either all individuals in a genomic dataset, or by ", + "training the model with one genomic dataset to predict the ", + "values in another." + ), + br(), br(), + bs4Dash::tabsetPanel( + id = "Genomic_Prediction_tabset", + tabPanel( + "Parameters description", + value = "Genomic_Prediction_par", + br(), + includeMarkdown( + system.file( + "help_files/Genomic_Prediction_par.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "Results description", + value = "Genomic_Prediction_results", + br(), + includeMarkdown( + system.file( + "help_files/Genomic_Prediction_res.Rmd", package = "BIGapp" + ) + ) + ), + tabPanel( + "How to cite", + value = "Genomic_Prediction_cite", + br(), + includeMarkdown( + system.file( + "help_files/Genomic_Prediction_cite.Rmd", package = "BIGapp" + ) + ) + ) + ) + ), ), - column(width=2) - # Add Help content here ) ) } - -#' help Server Functions -#' -#' @noRd -mod_help_server <- function(input, output, session, parent_session){ - - ns <- session$ns - -} - -## To be copied in the UI -# mod_help_ui("help_1") - -## To be copied in the server -# mod_help_server("help_1")