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Commit c774dd66 authored by svolant's avatar svolant
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modif curdir

parent 3f989bb8
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Rfunctions/DiagPlot.R
View file @ c774dd66
...@@ -541,6 +541,7 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))), ...@@ -541,6 +541,7 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
else Kval = val else Kval = val
ind_kept = which(as.character(group)%in%Kval) ind_kept = which(as.character(group)%in%Kval)
# save(val,Kval,dds,group_init,type.trans,VarInt,ind_kept,file="testLDA")
## Get the group corresponding to the modalities ## Get the group corresponding to the modalities
group = group[ind_kept] group = group[ind_kept]
nb = length(unique((group))) nb = length(unique((group)))
......
Rfunctions/VisuPlot.R
View file @ c774dd66
...@@ -812,5 +812,3 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table) ...@@ -812,5 +812,3 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table)
return(res) return(res)
} }
server.R
View file @ c774dd66
...@@ -30,7 +30,7 @@ shinyServer(function(input, output,session) { ...@@ -30,7 +30,7 @@ shinyServer(function(input, output,session) {
## Reactive target ## Reactive target
values <- reactiveValues(TargetWorking = target,labeled=NULL,fastq_names_only=NULL,R1fastQ=NULL,R2fastQ=NULL, values <- reactiveValues(TargetWorking = target,labeled=NULL,fastq_names_only=NULL,R1fastQ=NULL,R2fastQ=NULL,
json_name=json_name,num=0,pass=pass,login_email = NULL,is.valid =NULL, json_name=json_name,num=0,pass=pass,login_email = NULL,is.valid =NULL,
biom_masque = NULL,tree_masque=NULL,masque_key = NULL,paths_fastq_tmp=NULL) biom_masque = NULL,tree_masque=NULL,masque_key = NULL,paths_fastq_tmp=NULL,curdir=curdir)
## Counts file ## Counts file
dataInputCounts <-reactive({ dataInputCounts <-reactive({
...@@ -719,7 +719,7 @@ shinyServer(function(input, output,session) { ...@@ -719,7 +719,7 @@ shinyServer(function(input, output,session) {
CMP = CheckMasque(input, values) CMP = CheckMasque(input, values)
Error = CMP$Error Error = CMP$Error
isJSONalreadyExist = file.exists(paste(curdir,"www","masque","doing",basename(json_name),sep= .Platform$file.sep)) isJSONalreadyExist = file.exists(paste(values$curdir,"www","masque","doing",basename(json_name),sep= .Platform$file.sep))
if(is.null(Error) && !isJSONalreadyExist) if(is.null(Error) && !isJSONalreadyExist)
{ {
...@@ -1139,7 +1139,7 @@ shinyServer(function(input, output,session) { ...@@ -1139,7 +1139,7 @@ shinyServer(function(input, output,session) {
Error = CMP$Error Error = CMP$Error
if(is.null(Error) && isolate(values$num)<100){ if(is.null(Error) && isolate(values$num)<100){
progress_file = paste(curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_name)),"_progress",".txt",sep=""),sep= .Platform$file.sep) progress_file = paste(values$curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_name)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
if(file.exists(progress_file)) if(file.exists(progress_file))
{ {
pf = read_lines(progress_file) pf = read_lines(progress_file)
...@@ -1170,7 +1170,7 @@ shinyServer(function(input, output,session) { ...@@ -1170,7 +1170,7 @@ shinyServer(function(input, output,session) {
# #
# passOK = FALSE;status = NULL;file = NULL # passOK = FALSE;status = NULL;file = NULL
# print("OK") # print("OK")
# json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE) # json_files = list.files(paste(values$curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
# allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "") # allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "")
# #
# print(allpass) # print(allpass)
...@@ -1179,7 +1179,7 @@ shinyServer(function(input, output,session) { ...@@ -1179,7 +1179,7 @@ shinyServer(function(input, output,session) {
# passOK = any(isolate(input$password)==allpass) # passOK = any(isolate(input$password)==allpass)
# if(passOK){ # if(passOK){
# ind = which(isolate(input$password)==allpass) # ind = which(isolate(input$password)==allpass)
# file = paste(curdir,"www","masque",json_files[ind],sep= .Platform$file.sep) # file = paste(values$curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
# status = gsub(json_files[ind],pattern = "/.*",replacement = "") # status = gsub(json_files[ind],pattern = "/.*",replacement = "")
# } # }
# } # }
...@@ -1194,7 +1194,7 @@ shinyServer(function(input, output,session) { ...@@ -1194,7 +1194,7 @@ shinyServer(function(input, output,session) {
# #
# passOK = FALSE;status = NULL;file = NULL # passOK = FALSE;status = NULL;file = NULL
# #
# json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE) # json_files = list.files(paste(values$curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
# allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "") # allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "")
# #
# print(allpass) # print(allpass)
...@@ -1203,7 +1203,7 @@ shinyServer(function(input, output,session) { ...@@ -1203,7 +1203,7 @@ shinyServer(function(input, output,session) {
# passOK = any(isolate(values$pass)==allpass) # passOK = any(isolate(values$pass)==allpass)
# if(passOK){ # if(passOK){
# ind = which(values$pass==allpass) # ind = which(values$pass==allpass)
# file = paste(curdir,"www","masque",json_files[ind],sep= .Platform$file.sep) # file = paste(values$curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
# status = gsub(json_files[ind],pattern = "/.*",replacement = "") # status = gsub(json_files[ind],pattern = "/.*",replacement = "")
# } # }
# } # }
...@@ -1215,7 +1215,7 @@ shinyServer(function(input, output,session) { ...@@ -1215,7 +1215,7 @@ shinyServer(function(input, output,session) {
observeEvent(input$Check_project,{ observeEvent(input$Check_project,{
values$masque_key = input$password values$masque_key = input$password
resbox = Project_box_result(values$masque_key,curdir) resbox = Project_box_result(values$masque_key,values$curdir)
PS = resbox$PS PS = resbox$PS
passOK = PS$passOK passOK = PS$passOK
...@@ -1245,7 +1245,7 @@ shinyServer(function(input, output,session) { ...@@ -1245,7 +1245,7 @@ shinyServer(function(input, output,session) {
observeEvent(input$Check_project_over,{ observeEvent(input$Check_project_over,{
values$masque_key = values$pass values$masque_key = values$pass
resbox = Project_box_result(values$masque_key,curdir) resbox = Project_box_result(values$masque_key,values$curdir)
PS = resbox$PS PS = resbox$PS
passOK = PS$passOK passOK = PS$passOK
...@@ -1292,7 +1292,7 @@ shinyServer(function(input, output,session) { ...@@ -1292,7 +1292,7 @@ shinyServer(function(input, output,session) {
# folder_name = basename(file_path_sans_ext(json_file)) # folder_name = basename(file_path_sans_ext(json_file))
# print(folder_name) # print(folder_name)
# ### Paste file name as folder # ### Paste file name as folder
# annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep) # annot_process = paste(values$curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
# #
# if(file.exists(annot_process)) # if(file.exists(annot_process))
# { # {
...@@ -1323,7 +1323,7 @@ shinyServer(function(input, output,session) { ...@@ -1323,7 +1323,7 @@ shinyServer(function(input, output,session) {
# hideElement("project_over",anim=TRUE) # hideElement("project_over",anim=TRUE)
# #
# json_file = PS$file # json_file = PS$file
# error_file = paste(curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep) # error_file = paste(values$curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep)
# print(error_file) # print(error_file)
# if(file.exists(error_file)){error_message = read_lines(error_file)} # if(file.exists(error_file)){error_message = read_lines(error_file)}
# #
...@@ -1372,7 +1372,7 @@ shinyServer(function(input, output,session) { ...@@ -1372,7 +1372,7 @@ shinyServer(function(input, output,session) {
output$masque_status_key <-renderUI({ output$masque_status_key <-renderUI({
res = NULL res = NULL
resbox = Project_box_result(values$masque_key,curdir) resbox = Project_box_result(values$masque_key,values$curdir)
# if(resbox$PS$status=='done') showElement("MasqueToShaman",anim=TRUE) # if(resbox$PS$status=='done') showElement("MasqueToShaman",anim=TRUE)
# if(resbox$PS$status!='done') hideElement("MasqueToShaman",anim=TRUE) # if(resbox$PS$status!='done') hideElement("MasqueToShaman",anim=TRUE)
...@@ -1388,7 +1388,7 @@ shinyServer(function(input, output,session) { ...@@ -1388,7 +1388,7 @@ shinyServer(function(input, output,session) {
# folder_name = basename(file_path_sans_ext(json_file)) # folder_name = basename(file_path_sans_ext(json_file))
# print(folder_name) # print(folder_name)
# ### Paste file name as folder # ### Paste file name as folder
# annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep) # annot_process = paste(values$curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
# #
# if(file.exists(annot_process)) # if(file.exists(annot_process))
# { # {
...@@ -1417,7 +1417,7 @@ shinyServer(function(input, output,session) { ...@@ -1417,7 +1417,7 @@ shinyServer(function(input, output,session) {
# if(PS$status=="error"){ # if(PS$status=="error"){
# #
# json_file = PS$file # json_file = PS$file
# error_file = paste(curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep) # error_file = paste(values$curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep)
# print(error_file) # print(error_file)
# if(file.exists(error_file)){error_message = read_lines(error_file)} # if(file.exists(error_file)){error_message = read_lines(error_file)}
# #
...@@ -1445,7 +1445,7 @@ shinyServer(function(input, output,session) { ...@@ -1445,7 +1445,7 @@ shinyServer(function(input, output,session) {
res = NULL res = NULL
if(PS$status=="doing"){ if(PS$status=="doing"){
json_file = PS$file json_file = PS$file
progress_file = paste(curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_file)),"_progress",".txt",sep=""),sep= .Platform$file.sep) progress_file = paste(values$curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_file)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
if(file.exists(progress_file)) if(file.exists(progress_file))
{ {
pf = read_lines(progress_file) pf = read_lines(progress_file)
...@@ -1464,7 +1464,7 @@ shinyServer(function(input, output,session) { ...@@ -1464,7 +1464,7 @@ shinyServer(function(input, output,session) {
output$build_process_table <- DT::renderDataTable({ output$build_process_table <- DT::renderDataTable({
folder_name = paste('file',values$masque_key,sep="") folder_name = paste('file',values$masque_key,sep="")
build_process = paste(curdir,"www","masque","done",folder_name,"shaman_build_process.tsv",sep= .Platform$file.sep) build_process = paste(values$curdir,"www","masque","done",folder_name,"shaman_build_process.tsv",sep= .Platform$file.sep)
if(file.exists(build_process)) if(file.exists(build_process))
{ {
bp = read.csv(build_process,sep="\t",header=TRUE) bp = read.csv(build_process,sep="\t",header=TRUE)
...@@ -1588,8 +1588,8 @@ shinyServer(function(input, output,session) { ...@@ -1588,8 +1588,8 @@ shinyServer(function(input, output,session) {
observeEvent(input$RunResMasque,{ observeEvent(input$RunResMasque,{
updateSelectInput(session, "FileFormat","",selected = "fileBiom") updateSelectInput(session, "FileFormat","",selected = "fileBiom")
reset("fileBiom"); reset("fileTree") reset("fileBiom"); reset("fileTree")
values$biom_masque = paste(curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_",input$masque_database,".biom",sep=""),sep= .Platform$file.sep) values$biom_masque = paste(values$curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_",input$masque_database,".biom",sep=""),sep= .Platform$file.sep)
values$tree_masque = paste(curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_tree_",input$masque_database,".nhx",sep=""),sep= .Platform$file.sep) values$tree_masque = paste(values$curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_tree_",input$masque_database,".nhx",sep=""),sep= .Platform$file.sep)
}) })
...@@ -1598,7 +1598,7 @@ shinyServer(function(input, output,session) { ...@@ -1598,7 +1598,7 @@ shinyServer(function(input, output,session) {
output$Download_masque_zip <- downloadHandler( output$Download_masque_zip <- downloadHandler(
filename = function() { paste("SHAMAN_",values$masque_key,'.zip',sep="")}, filename = function() { paste("SHAMAN_",values$masque_key,'.zip',sep="")},
content = function(file){ content = function(file){
zip_file = paste(curdir,"www","masque","done",paste("file",values$masque_key,".zip",sep=""),sep= .Platform$file.sep) zip_file = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,".zip",sep=""),sep= .Platform$file.sep)
if(file.exists(zip_file)){file.copy(zip_file, file)} if(file.exists(zip_file)){file.copy(zip_file, file)}
} }
) )
......
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