marcelcosta/BDAccess
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Merge branch 'dev'

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Costa
2023-10-10 12:59:41 +02:00
parent 4c27e84cbd 560540cf1a
commit 9f7430a4ae
1 changed files with 25 additions and 12 deletions
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BDAccess/app.R
+24 -11
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@@ -144,24 +144,28 @@ server <- function(input, output) {
print(CCfile)
if (input$dbtype == "UM"){
dta<<-odbcConnectAccess2007(access.file = UMfile,
pwd = .rs.askForPassword("Enter password:"))
pwd = getPass::getPass("Enter password:"))
}
if (input$dbtype == "OV"){
dta<<-odbcConnectAccess2007(access.file = OVfile,
pwd = .rs.askForPassword("Enter password:"))
pwd = getPass::getPass("Enter password:"))
}
if (input$dbtype == "CC"){
dta<<-odbcConnectAccess2007(access.file = CCfile,
pwd = .rs.askForPassword("Enter password:"))
pwd = getPass::getPass("Enter password:"))
}
print(dta)
if (input$backup == T){
if (! input$dbtype %in% c("UM","OV")){
sqlBackUp(bu.dir="CC_BU")
}else{
sqlBackUp()
sqlBackUp(dbfile = CCfile, bu.dir="CC_BU")
}
if (input$dbtype == "UM"){
sqlBackUp(dbfile = UMfile)
}
if (input$dbtype == "OV"){
sqlBackUp(dbfile = OVfile)
}
print("Back up realizado.")
}
})
@@ -380,7 +384,7 @@ server <- function(input, output) {
new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "samples"=new.samp) %>% merge(sqlFetch(dta,"OVID", as.is=T), all.x=T) %>% arrange(samples)
samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
if (today==TRUE){
samples.exp$IQ_date<-format(Sys.Date(), "%d/%m/%y")
samples.exp$Date_extraction<-format(Sys.Date(), "%d/%m/%y")
}
nhc.table<-values[["DF"]]
@@ -754,6 +758,7 @@ server <- function(input, output) {
sqlFetch(dta, "NITROGEN"),
file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","UM-Nitrogen.xlsx")
)
print("Backup Creado.")
table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
@@ -784,6 +789,7 @@ server <- function(input, output) {
sqlDrop(dta, "NITROGEN")
sqlSave(dta, table.um %>% select(-FECHA) %>% filter(!is.na(CODIGO)), tablename="NITROGEN", rownames=F)
print("Tabla Actualizada.")
}
if (input$dbtype == "OV"){
## Copia de backup
@@ -797,6 +803,7 @@ server <- function(input, output) {
sqlFetch(dta, "NITROGEN"),
file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","OV-Nitrogen.xlsx")
)
print("Backup Creado.")
## Lectura del excel
table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
@@ -822,6 +829,7 @@ server <- function(input, output) {
sqlDrop(dta, "NITROGEN")
sqlSave(dta, table.ov, tablename="NITROGEN", rownames=F)
print("Tabla Actualizada.")
}
})
@@ -924,9 +932,14 @@ server <- function(input, output) {
pops<-sqlFetch(dta, "POPULATIONS")
g_pop<-pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>%
mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
"CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
g_pop<-pops %>%
dplyr::filter(sample == input$id) %>%
gather(pop,value,-sample, -code, -fc_time) %>%
# mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
# "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
# mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
# "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
mutate(value=as.numeric(gsub(",",".",value))) %>%
ggplot(aes(pop, value))+
geom_bar(stat="identity", color="black", fill="grey70")+
labs(title = input$id, y="% parent", x="")+