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Merged
Cristianetaniguti merged 1 commit into from
Apr 29, 2026
Merged

rm Qploidy #13

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: Breedverse
Title: Collection of R Shiny Packages From Breeding Insight
Version: 0.3.0
Version: 0.3.1
Authors@R: c(person(given='Cristiane',
family='Taniguti',
email = 'ctaniguti@ufl.edu',
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4 changes: 4 additions & 0 deletions NEWS.md
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@@ -1,5 +1,9 @@
# breedverse NEWS

## breedverse 0.3.1

* Remove Qploidy while it is going throught repository transition

## breedverse 0.3.0

* Add GenoBrew
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20 changes: 10 additions & 10 deletions R/app_server.R
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Expand Up @@ -14,9 +14,9 @@ app_server <- function(input, output, session) {
options(shiny.maxRequestSize = 1000000 * 1024^2) # Set maximum upload size to 1000GB
#shiny.maxRequestSize = 10000 * 1024^2; # 10 GB <- This is for a future limit when using BI's server remotely

output$qploidyInstalled <- reactive({
"Qploidy" %in% rownames(installed.packages())
})
# output$qploidyInstalled <- reactive({
# "Qploidy" %in% rownames(installed.packages())
# })

output$BIGappInstalled <- reactive({
"BIGapp" %in% rownames(installed.packages())
Expand All @@ -35,7 +35,7 @@ app_server <- function(input, output, session) {
})

# Expose the value to JS even when panel is hidden
outputOptions(output, "qploidyInstalled", suspendWhenHidden = FALSE)
# outputOptions(output, "qploidyInstalled", suspendWhenHidden = FALSE)
outputOptions(output, "BIGappInstalled", suspendWhenHidden = FALSE)
outputOptions(output, "familiaInstalled", suspendWhenHidden = FALSE)
outputOptions(output, "allomateInstalled", suspendWhenHidden = FALSE)
Expand All @@ -55,12 +55,12 @@ app_server <- function(input, output, session) {
parent_session = session)

## Qploidy
if(isTRUE(requireNamespace("Qploidy", quietly = TRUE))) {
do.call("library", list("Qploidy"))
callModule(getFromNamespace("mod_qploidy_server", "Qploidy"),
"qploidy_1",
parent_session = session)
}
# if(isTRUE(requireNamespace("Qploidy", quietly = TRUE))) {
# do.call("library", list("Qploidy"))
# callModule(getFromNamespace("mod_qploidy_server", "Qploidy"),
# "qploidy_1",
# parent_session = session)
# }

## BIGapp

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20 changes: 10 additions & 10 deletions R/app_ui.R
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Expand Up @@ -58,11 +58,11 @@ app_ui <- function(request) {
menuItem("Home", tabName = "welcome", icon = icon("house"),startExpanded = FALSE),
menuItem("Install modules", tabName = "install", icon = icon("share-from-square")),

conditionalPanel(
condition = "output.qploidyInstalled == true",
tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Ploidy Estimation"),
menuItem("Qploidy", tabName = "qploidy", icon = icon("dna")),
),
# conditionalPanel(
# condition = "output.qploidyInstalled == true",
# tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Ploidy Estimation"),
# menuItem("Qploidy", tabName = "qploidy", icon = icon("dna")),
# ),

conditionalPanel(
condition = "output.familiaInstalled == true",
Expand Down Expand Up @@ -151,11 +151,11 @@ app_ui <- function(request) {
tabItem(
tabName = "install", mod_install_ui("install_1")
),
tabItem(
tabName = "qploidy",
if(isTRUE(requireNamespace("Qploidy", quietly = TRUE)))
getFromNamespace("mod_qploidy_ui", "Qploidy")("qploidy_1")
),
# tabItem(
# tabName = "qploidy",
# if(isTRUE(requireNamespace("Qploidy", quietly = TRUE)))
# getFromNamespace("mod_qploidy_ui", "Qploidy")("qploidy_1")
# ),
tabItem(
tabName = "snmf",
if(isTRUE(requireNamespace("familia", quietly = TRUE)))
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38 changes: 19 additions & 19 deletions R/mod_help.R
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Expand Up @@ -13,23 +13,23 @@ mod_help_ui <- function(id){
fluidPage(
column(width=12),
column(width=12,
conditionalPanel(
condition = "output.qploidyInstalled == true",
box(title="Ploidy Estimation", id = "Qploidy_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE,
"This tab uses Qploidy package to standardize marker allele counts to estimate ploidy or aneuploidy.",
br(), br(),
bs4Dash::tabsetPanel(id = "Qploidy_tabset",
tabPanel("Parameters description", value = "Qploidy_par", br(),
includeMarkdown(system.file("help_files/Qploidy_par.Rmd", package = "Qploidy"))
),
tabPanel("Results description", value = "Qploidy_results", br(),
includeMarkdown(system.file("help_files/Qploidy_res.Rmd", package = "Qploidy"))
),
tabPanel("How to cite", value = "Qploidy_cite", br(),
includeMarkdown(system.file("help_files/Qploidy_cite.Rmd", package = "Qploidy"))
))
)
),
# conditionalPanel(
# condition = "output.qploidyInstalled == true",
# box(title="Ploidy Estimation", id = "Qploidy_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE,
# "This tab uses Qploidy package to standardize marker allele counts to estimate ploidy or aneuploidy.",
# br(), br(),
# bs4Dash::tabsetPanel(id = "Qploidy_tabset",
# tabPanel("Parameters description", value = "Qploidy_par", br(),
# includeMarkdown(system.file("help_files/Qploidy_par.Rmd", package = "Qploidy"))
# ),
# tabPanel("Results description", value = "Qploidy_results", br(),
# includeMarkdown(system.file("help_files/Qploidy_res.Rmd", package = "Qploidy"))
# ),
# tabPanel("How to cite", value = "Qploidy_cite", br(),
# includeMarkdown(system.file("help_files/Qploidy_cite.Rmd", package = "Qploidy"))
# ))
# )
# ),
conditionalPanel(
condition = "output.BIGappInstalled == true",
box(title="Convert to VCF", id = "DArT_Report2VCF_box",width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE,
Expand Down Expand Up @@ -170,9 +170,9 @@ mod_help_ui <- function(id){
#'
#' @noRd
mod_help_server <- function(input, output, session, parent_session){

ns <- session$ns

}

## To be copied in the UI
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