Commit 5a3c68ab authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Split 16S and 18S

parent 9540f3d4
......@@ -48,8 +48,8 @@ Project_box_result <- function(masque_key,curdir){
if(file.exists(annot_process))
{
ap = read.csv(annot_process,sep="\t")
if(json_data[[1]]$type == "16S_18S") db_choices = c("Silva" = "silva","Greengenes" = "greengenes", "RDP"= "rdp")
else if(json_data[[1]]$type == "23S_28S") db_choices = c("Silva" = "silva","RDP"= "rdp")
if(json_data[[1]]$type == "16S") db_choices = c("Silva" = "silva","Greengenes" = "greengenes", "RDP"= "rdp")
else if(json_data[[1]]$type == "23S_28S" || json_data[[1]]$type == "18S") db_choices = c("Silva" = "silva","RDP"= "rdp")
else db_choices = c("Findley" = "findley", "Underhill"= "underhill", "Unite"= "unite", "RDP"= "rdp")
#build_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_annotation.tsv",sep= .Platform$file.sep)
res[[1]] = fluidRow(
......@@ -65,14 +65,21 @@ Project_box_result <- function(masque_key,curdir){
shinydashboard::valueBox(ap$Count[5],tags$strong(tags$h5("Number of OTU", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("otu_icon"))
),
#column(width=5, div(img(src = "masque.png",width = "50%",height = "20%"))),
if(json_data[[1]]$type == "16S_18S"){
if(json_data[[1]]$type == "16S"){
column(width=5,
strong(h3("16S/18S annotation process")),
strong(h3("16S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by Greengenes", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("greengenes_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else if(json_data[[1]]$type == "18S"){
column(width=5,
strong(h3("18S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else if(json_data[[1]]$type == "23S_28S"){
column(width=5,
strong(h3("23S/28S annotation process")),
......
......@@ -304,7 +304,7 @@ body <- dashboardBody(
div(id="masque-form",
box(title="About",width = NULL, status = "primary",
column(width=6, radioButtons("DataTypeMasque",label = "Type of data",choices = c("16S/18S" = "16S_18S","23S/28S" = "23S_28S","ITS" = "ITS"),inline = TRUE)),
column(width=6, radioButtons("DataTypeMasque",label = "Type of data",choices = c("16S" = "16S", "18S" = "18S","23S/28S" = "23S_28S","ITS" = "ITS"),inline = TRUE)),
column(width=6, radioButtons("PairedOrNot",label = "Paired-end sequencing ?",choices = c('Yes'="y","No"="n"),selected = "n",inline = TRUE)),
column(width=3, textInput("to", "Email address *", value="yyy@xxx"),
bsTooltip("to", "Enter a valid email address to get your results","bottom",trigger = "hover", options = list(container = "body"))
......
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