Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Organize GWAS tabs #71

Merged
merged 3 commits into from
Sep 25, 2024
Merged

Organize GWAS tabs #71

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
48dada1
Merge pull request #17 from Breeding-Insight/development
Cristianetaniguti Sep 25, 2024
6cabc78
organize GWAS tabs #70
Cristianetaniguti Sep 25, 2024
d38e38a
table with all QTL + only one model for fit.qtl #70
Cristianetaniguti Sep 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
187 changes: 123 additions & 64 deletions R/mod_gwas.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ mod_gwas_ui <- function(id){
fileInput(ns("gwas_file"), "Choose VCF File", accept = c(".csv",".vcf",".gz")),
fileInput(ns("phenotype_file"), "Choose Passport File", accept = ".csv"),
numericInput(ns("gwas_ploidy"), "Species Ploidy", min = 1, value = NULL),
numericInput(ns("bp_window_before"), "Base pair window", min = 0, value = 5e6),
numericInput(ns("bp_window_before"), "Base pair window", min = 0, value = 50),
selectInput(ns('gwas_threshold'), label='Significance Threshold Method', choices = c("M.eff","Bonferroni","FDR","permute"), selected="M.eff"),
selectInput(ns('trait_info'), label = 'Select Trait (eg. Color):', choices = NULL),
virtualSelectInput(
Expand Down Expand Up @@ -53,26 +53,46 @@ mod_gwas_ui <- function(id){
),
column(width = 6,
box(
title = "Plots", status = "info", solidHeader = FALSE, width = 12, height = 800,
title = "Plots", status = "info", solidHeader = FALSE, width = 12,
bs4Dash::tabsetPanel(
tabPanel("Linkage Desiquilibrium Plot",
withSpinner(plotOutput(ns("LD_plot"), height = "500px")), br(),
conditionalPanel(
condition = "input.gwas_start", ns = ns,
div(
sliderInput(ns("bp_window_after"), label = "Adjust base pair window here and run analysis again", min = 0,
max = 100e6, value = 5e6, step = 100),
)
)
),
tabPanel("BIC Plot", withSpinner(plotOutput(ns("bic_plot"), height = "500px"))),
tabPanel("Manhattan Plot", withSpinner(plotOutput(ns("manhattan_plot"), height = "500px"))),
tabPanel("QQ Plot", withSpinner(plotOutput(ns("qq_plot"), height = "500px"))),
tabPanel("BIC Table", withSpinner(DTOutput(ns("bic_table"))),style = "overflow-y: auto; height: 500px"),
tabPanel("QTL - significant markers",
withSpinner(DTOutput(ns('gwas_stats'))),style = "overflow-y: auto; height: 500px"),
tabPanel("Multiple QTL model results table",
withSpinner(DTOutput(ns('gwas_fitqtl'))),style = "overflow-y: auto; height: 500px")
tabPanel("QTL - significant markers", withSpinner(DTOutput(ns("all_qtl"))),style = "overflow-y: auto; height: 500px"),
tabPanel("Filter QTL by LD window",
br(),
box(
title = "LD plot",solidHeader = FALSE, width = 12,
withSpinner(plotOutput(ns("LD_plot"), height = "500px")), br(),
sliderInput(ns("bp_window_after"), label = "Adjust base pair window here and run analysis again", min = 0,
max = 100e6, value = 50, step = 100)
),
box(
title = "Filtered QTL", solidHeader = FALSE, width = 12,
withSpinner(DTOutput(ns('gwas_stats')))
)
),
tabPanel("Multiple QTL model",
br(),
pickerInput(
inputId = ns("sele_models"),
label = "Select model",
choices = "will be updated",
options = list(
`actions-box` = TRUE),
multiple = FALSE
), hr(),
pickerInput(
inputId = ns("sele_qtl"),
label = "Select QTL",
choices = "will be updated",
options = list(
`actions-box` = TRUE),
multiple = TRUE
), hr(),
withSpinner(DTOutput(ns('gwas_fitqtl'))),
style = "overflow-y: auto; height: 500px")
)
)
),
Expand Down Expand Up @@ -164,8 +184,14 @@ mod_gwas_server <- function(input, output, session, parent_session){
output$gwas_stats <- renderDT(NULL)

##GWAS items
gwas_data <- reactiveValues(
data2 = NULL,
phenos = NULL
)

gwas_vars <- reactiveValues(
gwas_df = NULL,
gwas_df_filt = NULL,
fit_qtl = NULL,
manhattan_plots = NULL,
LD_plot = NULL,
Expand Down Expand Up @@ -194,7 +220,6 @@ mod_gwas_server <- function(input, output, session, parent_session){

#GWAS analysis (Shufen Chen and Meng Lin pipelines)
observeEvent(input$gwas_start, {

toggleClass(id = "gwas_ploidy", class = "borderred", condition = (is.na(input$gwas_ploidy) | is.null(input$gwas_ploidy)))
toggleClass(id = "trait_info", class = "borderred", condition = (all(is.na(input$trait_info)) | all(is.null(input$trait_info))))

Expand Down Expand Up @@ -373,7 +398,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
)

gwas_vars$bp_window <- input$bp_window_before
updateSliderInput(session = session, inputId = "bp_window_after", min = 0, max = lim.d, value = gwas_vars$bp_window, step = round(lim.d/30,4))
updateSliderInput(session = session, inputId = "bp_window_after", min = 0, max = round(lim.d,2), value = gwas_vars$bp_window, step = round(lim.d/30,4))

data.loco <- set.K(data,LOCO=F,n.core= as.numeric(cores))

Expand Down Expand Up @@ -414,6 +439,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
kin.adj<-posdefmat(K)
kin.test<-as.matrix(kin.adj)

phenos <- vector()
for (i in 2:ncol(GE)){

#model selection
Expand Down Expand Up @@ -465,46 +491,13 @@ mod_gwas_server <- function(input, output, session, parent_session){
#Consider adding options for different thresholds
data2 <- set.threshold(data.loco.scan,method=input$gwas_threshold,level=0.05)


#Save manhattan plots to list (only for single trait analysis)
#if length(traits) == 1
manhattan_plot_list <- list()

#plot for six models per trait
manhattan_plot_list[["all"]] <- manhattan.plot(data2,traits=colnames(data@pheno[i]), models = model)+geom_point(size=3)+theme(text = element_text(size = 25),strip.text = element_text(face = "bold"))

#get most significant SNPs per QTL file
print("Used")
print(gwas_vars$bp_window)
qtl <- get.QTL(data=data2,traits=colnames(data@pheno[i]),bp.window=gwas_vars$bp_window)
qtl_d <- data.frame(qtl)

#Save QTL info
gwas_vars$gwas_df <- qtl_d

if(length(qtl$Model) >0){
rm.qtl <- which(qtl$Model %in% c("diplo-general", "diplo-additive"))
if(length(rm.qtl) > 0){
warning("QTL detected by the models diplo-general and diplo-additive are not supported in the fit.QTL current version")
qtl <- qtl[-rm.qtl,]
}

fit.ans_temp <- fit.QTL(data=data2,
trait=input$trait_info,
qtl=qtl[,c("Marker","Model")])
gwas_vars$fit_qtl <- fit.ans_temp
} else gwas_vars$fit_qtl <- NULL

#Updating value boxes
output$qtls_detected <- renderValueBox({
valueBox(
value = length(unique(qtl_d$Position)),
subtitle = "QTLs Detected",
icon = icon("dna"),
color = "info"
)
})

#Status
updateProgressBar(session = session, id = "pb_gwas", value = 80, title = "GWAS Complete: Now Plotting Results")

Expand All @@ -525,28 +518,80 @@ mod_gwas_server <- function(input, output, session, parent_session){

#Save manhattan plots
gwas_vars$manhattan_plots <- manhattan_plot_list

phenos[i] <- colnames(data@pheno[i])
}

gwas_data$data2 <- data2
gwas_data$phenos <- phenos[-which(is.na(phenos))]

qtl <- get.QTL(data=gwas_data$data2,traits=gwas_data$phenos,bp.window=0)
gwas_vars$gwas_df <- data.frame(qtl)

#Status
updateProgressBar(session = session, id = "pb_gwas", value = 100, status = "success", title = "Finished")
})

#Updating value boxes
output$qtls_detected <- renderValueBox({
valueBox(
value = length(unique(gwas_vars$gwas_df$Position)),
subtitle = "QTLs Detected",
icon = icon("dna"),
color = "info"
)
})

# Tables
output$gwas_stats <- renderDT({
output$all_qtl <- renderDT({
#get most significant SNPs per QTL file
validate(
need(dim(gwas_vars$gwas_df)[1] > 0, "No QTL detected.")
)
gwas_vars$gwas_df
}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))


output$gwas_stats <- renderDT({
#get most significant SNPs per QTL file
lim.d <- max(gwas_vars$LD_plot$data$d)

validate(
need(gwas_vars$bp_window <= lim.d, paste0("Base pair window larger than maximum distance (",lim.d,"). Reduce window size."))
)
if(is.null(input$bp_window_after)) {
line <- gwas_vars$bp_window
} else line <- input$bp_window_after

qtl <- get.QTL(data=gwas_data$data2,traits=gwas_data$phenos,bp.window=line*1000000)
gwas_vars$gwas_df_filt <- data.frame(qtl)

validate(
need(dim(gwas_vars$gwas_df_filt)[1] > 0, "No QTL detected.")
)
gwas_vars$gwas_df_filt
}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))


observe({
req(gwas_vars$gwas_df_filt)
updatePickerInput(session = session, inputId = "sele_models", choices = unique(gwas_vars$gwas_df_filt$Model), selected = unique(gwas_vars$gwas_df_filt$Model)[1])
})

observe({
req(gwas_vars$gwas_df_filt)
df <- gwas_vars$gwas_df_filt %>% filter(Model %in% input$sele_models)
updatePickerInput(session = session, inputId = "sele_qtl", choices = unique(paste0(df$Marker, "_", df$Model)),
selected = unique(paste0(df$Marker, "_", df$Model)))
})

output$gwas_fitqtl <- renderDT({
validate(
need(dim(gwas_vars$gwas_df)[1] > 0, "No QTL detected.")
need(dim(gwas_vars$gwas_df_filt)[1] > 0, "No QTL detected.")
)

rm.qtl <- which(gwas_vars$gwas_df$Model %in% c("diplo-general", "diplo-additive"))
df <- gwas_vars$gwas_df_filt[which(paste0(gwas_vars$gwas_df_filt$Marker, "_", gwas_vars$gwas_df_filt$Model) %in% input$sele_qtl),]

rm.qtl <- which(df$Model %in% c("diplo-general", "diplo-additive"))
if(length(rm.qtl) > 0){
shinyalert(
title = "Oops",
Expand All @@ -565,11 +610,25 @@ mod_gwas_server <- function(input, output, session, parent_session){
)
}

gwas_vars$fit_qtl
}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))
if(length(df$Model) >0){
rm.qtl <- which(df$Model %in% c("diplo-general", "diplo-additive"))
if(length(rm.qtl) > 0){
warning("QTL detected by the models diplo-general and diplo-additive are not supported in the fit.QTL current version")
qtl <- df[-rm.qtl,]
} else qtl <- df

validate(
need(dim(qtl)[1] > 0, "No QTL evaluated")
)

fit.ans_temp <- fit.QTL(data=gwas_data$data2,
trait=input$trait_info,
qtl=qtl[,c("Marker","Model")])
gwas_vars$fit_qtl <- fit.ans_temp
} else gwas_vars$fit_qtl <- NULL

gwas_vars$fit_qtl
}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))

# Plots
#Output the manhattan plots
Expand Down Expand Up @@ -636,10 +695,10 @@ mod_gwas_server <- function(input, output, session, parent_session){
temp_dir <- tempdir()
temp_files <- c()

if (!is.null(gwas_vars$gwas_df)) {
if (!is.null(gwas_vars$gwas_df_filt)) {
# Create a temporary file for assignments
gwas_file <- file.path(temp_dir, paste0("QTL-statistics-", Sys.Date(), ".csv"))
write.csv(gwas_vars$gwas_df, gwas_file, row.names = FALSE)
write.csv(gwas_vars$gwas_df_filt, gwas_file, row.names = FALSE)
temp_files <- c(temp_files, gwas_file)
}

Expand Down Expand Up @@ -728,14 +787,14 @@ mod_gwas_server <- function(input, output, session, parent_session){
ex <- system.file("iris_passport_file.csv", package = "BIGapp")
file.copy(ex, file)
})

##Summary Info
gwas_summary_info <- function() {
#Handle possible NULL values for inputs
dosage_file_name <- if (!is.null(input$gwas_file$name)) input$gwas_file$name else "No file selected"
passport_file_name <- if (!is.null(input$phenotype_file$name)) input$phenotype_file$name else "No file selected"
selected_ploidy <- if (!is.null(input$gwas_ploidy)) as.character(input$gwas_ploidy) else "Not selected"

#Print the summary information
cat(
"BIGapp GWAS Summary\n",
Expand Down Expand Up @@ -766,7 +825,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
sep = ""
)
}

# Popup for analysis summary
observeEvent(input$gwas_summary, {
showModal(modalDialog(
Expand All @@ -782,8 +841,8 @@ mod_gwas_server <- function(input, output, session, parent_session){
)
))
})


# Download Summary Info
output$download_gwas_info <- downloadHandler(
filename = function() {
Expand Down
Loading