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Añadir sección de citometría para tinciones de Poblaciones.

main
marcelcosta 2 years ago
parent
commit
67ba4921ca
1 changed files with 71 additions and 12 deletions
  1. +71
    -12
      BDAccess/app.R

+ 71
- 12
BDAccess/app.R

@ -5,6 +5,10 @@ library(reshape2)
library(Matrix) library(Matrix)
library(CitFuns) library(CitFuns)
library(BDCIT) library(BDCIT)
library(openCyto)
library(flowCore)
library(flowWorkspace)
library(CytoML)
print(getwd()) print(getwd())
source("../sqlFunctions.R", encoding = "UTF-8") source("../sqlFunctions.R", encoding = "UTF-8")
@ -76,19 +80,16 @@ ui <- fluidPage(
## Citometría ---- ## Citometría ----
tabPanel("Citometría", tabPanel("Citometría",
sidebarPanel( sidebarPanel(
# shinyDirButton(id="cito_dir",label="Cito Dir", title="Citometría")
# fileInput(inputId = "cito_dir", label = "Cito Dir", multiple = F)
selectInput("phenotype", "Tipo de análisis", selected="Pop", choices=c("Pop", "IC")),
), ),
mainPanel( mainPanel(
actionButton("goButtonDir","load session to analyze"),
textOutput("session")
# tabsetPanel(
# tabPanel("Table", tableOutput("sc_table")),
# tabPanel("Plots",
# plotOutput("sc_plot", height = "1000px"),
# plotOutput("sc_expr"), height = "600px")
# )
actionButton("goButtonDir","Selecciona directorio fenotipo"),
textOutput("session"),
hr(),
actionButton("fcsconvert", "Convertir a fcs"),
hr(),
actionButton("pngexport", "Exportar informes"),
actionButton("popexport", "Actualizar BBDD")
) )
), ),
@ -820,7 +821,7 @@ server <- function(input, output) {
observe({ observe({
if(input$goButtonDir > 0){ if(input$goButtonDir > 0){
cito_dir<<-choose.dir() %>% gsub("\\","/",. ,fixed=T)
cito_dir<<-choose.dir() %>% gsub("\\","/",. ,fixed=T) %>% paste0("/")
output$session <- renderText( output$session <- renderText(
cito_dir cito_dir
@ -828,6 +829,64 @@ server <- function(input, output) {
} }
}) })
observeEvent(input$fcsconvert,{
route<-cito_dir
files<-list.files(route, ".LMD")
for (lmd in files){
fcs<-read.FCS(paste0(route,lmd), dataset = 2)
# fcs@parameters$desc<-c("FS-A","SS-A", paste("FL",1:10,"-A", sep = ""), "TIME")
# fcs@parameters$desc<-c("FS-H","FS-A","FS-W","SS-H","SS-A","TIME", paste("FL",1:10,"-A", sep = ""))
keyword(fcs)['$FIL']<-paste0(gsub(".LMD","",lmd), ".fcs")
write.FCS(fcs, paste0(route, gsub(".LMD","",lmd), ".fcs"))
}
})
observeEvent(input$pngexport,{
route<-cito_dir
ws<-open_flowjo_xml(paste0(route,"Populations.wsp"))
gs<-flowjo_to_gatingset(ws, name="All Samples")
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>%
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
for (samp in sampleNames(gs)){
print(samp)
p<-autoplot(gs[[samp]], bins=64)
ggsave(paste0(route, samp,".png"),p,width = 10, height = 10)
}
})
observeEvent(input$popexport,{
route<-cito_dir
ws<-open_flowjo_xml(paste0(route,"Populations.wsp"))
gs<-flowjo_to_gatingset(ws, name="All Samples")
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>%
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1)
nodes<-nodes[grepl("_",nodes)]
pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100)
pop[,"pop"]<-gsub("_","",pop$pop)
pop$pop<-gsub(" ","_",pop$pop)
pop$pop<-gsub("+","pos",pop$pop, fixed=T)
pop$pop<-gsub("-","neg",pop$pop, fixed=T)
pop<-rename(pop, "samples"="sample")
pop$percent<-round(pop$percent, digits=2)
pop_sp<-pop %>% spread(pop, percent)
vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length)
names(vartypes)<-pop_sp %>% select(-samples) %>% colnames
sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F)
print("Tabla POPULATIONS sincronizada.")
})
## scRNAseq ---- ## scRNAseq ----

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