gin commit from med068pc183

New files: 1

Codes/meaRtools/.Rhistory

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+source('D:/gin-cli-latest-windows64/attempt2/Codes/meaRtools/MEA_analysis_Axion.R')
+library(svDialogs)
+Filesdirectory<-paste0(choose.dir(default = "", caption = "SELECT THE FOLDER WITH THE FILES"),"\\")
+#my.files2 <- as.list(choose.files(default = "", caption = "SELECT YOUR SPIKE FILES", multi = TRUE))#,
+my.files2=as.list(list.files(Filesdirectory, full.names=TRUE))
+WorF <- (dlgInput("Enter your experiment type:  (w) for weekly and (p) for pharma")$res)#, Sys.info()["user"])$res
+View(my.files2)
+my.files2[[1]]
+my.files2[[2]]
+my.files2[[3]]
+if (WorF == 'w') {
+pattern="week\\s\\d{1}"
+string=Filesdirectory
+DIV=regmatches(string, regexpr(pattern, string))
+DIV=paste0('DIV',gsub(" ", "", DIV, fixed = TRUE))
+ExpName='beforePFF'
+} else if (WorF == 'p') {
+dday=regmatches(Filesdirectory, regexpr('\\+\\d+', Filesdirectory))
+ExpName=paste0('PFFday',gsub("+", "", dday, fixed = TRUE))
+} else {
+stop("Please, enter the appropriate experiment type: (w) for weekly and (p) for pharma!")
+}
+library(svDialogs)
+Filesdirectory<-paste0(choose.dir(default = "", caption = "SELECT THE FOLDER WITH THE FILES"),"\\")
+#my.files2 <- as.list(choose.files(default = "", caption = "SELECT YOUR SPIKE FILES", multi = TRUE))#,
+my.files2=as.list(list.files(Filesdirectory, full.names=TRUE))
+WorF <- (dlgInput("Enter your experiment type:  (w) for weekly and (p) for pharma")$res)#, Sys.info()["user"])$res
+if (WorF == 'w') {
+pattern="week\\s\\d{1}"
+string=Filesdirectory
+DIV=regmatches(string, regexpr(pattern, string))
+DIV=paste0('DIV',gsub(" ", "", DIV, fixed = TRUE))
+ExpName='beforePFF'
+} else if (WorF == 'p') {
+dday=regmatches(Filesdirectory, regexpr('\\+\\d+', Filesdirectory))
+ExpName=paste0('PFFday',gsub("+", "", dday, fixed = TRUE))
+} else {
+stop("Please, enter the appropriate experiment type: (w) for weekly and (p) for pharma!")
+}
+my.channels2=my.explog <- choose.files(default = "", caption = "SELECT YOUR POSITION FILE (e.g. 1well_8x8.csv or so)", multi = FALSE)
+my.input2 <- choose.dir(default = "", caption = "SELECT YOUR OUTPUT FOLDER")
+#my.channel_text_file <- '1well_8x8.csv' # name of your positions file - add .csv to end !!
+# note that channel_text_file determines the well information you wish to use
+# inform the number of wells - this will be added to the exported file name
+my.well_number <- '6w' # e.g. '6w' or '1w'
+# extracting data
+my.spike_data <- list()
+for (i in 1:length(my.files2)) {
+my.spike_data[[i]] <- read.csv(my.files2[[i]])
+}
+my.channel_data <- read.csv(my.channels2, stringsAsFactors = FALSE)
+# creating new spike data with well indo added to the electrode name
+new.channels <- my.channel_data$Channel
+new.ch <- list()
+for (i in 1:length(my.spike_data)) {
+new.ch[[i]] <- rep(0, times = length(my.spike_data[[i]]$Channel))
+for (k in 1:length(new.channels)) {
+new.ch[[i]][which(my.spike_data[[i]]$Channel == strsplit(new.channels[k], split = '_')[[1]][2])] <- new.channels[k]
+}
+}
+new.times <- list()
+for (i in 1:length(my.spike_data)) {
+new.times[[i]] <- my.spike_data[[i]]$Time
+}
+# creating and exporting data frames as csv
+for (i in 1:length(my.spike_data)) {
+new.df <- data.frame()
+new.df <- data.frame('Channel' = new.ch[[i]], 'Time' = new.times[[i]])
+#new.basename <- c()
+#new.basename <- strsplit(basename(my.files2[[i]]), split = '.csv')[[1]][1]
+if (WorF == 'p') {
+pattern3="baseline1|baseline2|AMPA|CNQX|NMDA|DAP5"
+DIV=regmatches(basename(my.files2[[i]]), regexpr(pattern3, basename(my.files2[[i]])))
+DIV=paste0('DIV',DIV)
+}
+pattern2="N\\d{3,}"
+plateN=regmatches(basename(my.files2[[i]]), regexpr(pattern2,basename(my.files2[[i]])))
+CHECKTHIS THING!!!ExpDate="210226"
+#=regmatches(basename(my.files2[[i]]), regexpr('\\d{5,}', basename(my.files2[[i]])))
+export_name <- paste0(my.input2, '/',plateN, '_', ExpDate, '_', ExpName,'_', DIV, '_', 'spikes', '_', my.well_number, '.csv')
+#export_name <- paste0(my.input2, '/',new.basename, '_', my.well_number, '.csv')
+write.csv(new.df, file = export_name, row.names = FALSE, quote = FALSE)
+}
+# creating and exporting data frames as csv
+for (i in 1:length(my.spike_data)) {
+new.df <- data.frame()
+new.df <- data.frame('Channel' = new.ch[[i]], 'Time' = new.times[[i]])
+#new.basename <- c()
+#new.basename <- strsplit(basename(my.files2[[i]]), split = '.csv')[[1]][1]
+if (WorF == 'p') {
+pattern3="baseline1|baseline2|AMPA|CNQX|NMDA|DAP5"
+DIV=regmatches(basename(my.files2[[i]]), regexpr(pattern3, basename(my.files2[[i]])))
+DIV=paste0('DIV',DIV)
+}
+pattern2="N\\d{3,}"
+plateN=regmatches(basename(my.files2[[i]]), regexpr(pattern2,basename(my.files2[[i]])))
+CHECKTHIS THING!!!ExpDate="210226"
+#=regmatches(basename(my.files2[[i]]), regexpr('\\d{5,}', basename(my.files2[[i]])))
+export_name <- paste0(my.input2, '/',plateN, '_', ExpDate, '_', ExpName,'_', DIV, '_', 'spikes', '_', my.well_number, '.csv')
+#export_name <- paste0(my.input2, '/',new.basename, '_', my.well_number, '.csv')
+write.csv(new.df, file = export_name, row.names = FALSE, quote = FALSE)
+}
+View(my.files2)
+my.files2[[1]]
+pattern2="N\\d{3,}"
+plateN=regmatches(basename(my.files2[[1]]), regexpr(pattern2,basename(my.files2[[1]])))
+regmatches(basename(my.files2[[1]]), regexpr('\\d{5,}', basename(my.files2[[1]])))
+ExpDate=regmatches(basename(my.files2[[1]]), regexpr('\\d{5,}', basename(my.files2[[1]])))
+# creating and exporting data frames as csv
+for (i in 1:length(my.spike_data)) {
+new.df <- data.frame()
+new.df <- data.frame('Channel' = new.ch[[i]], 'Time' = new.times[[i]])
+#new.basename <- c()
+#new.basename <- strsplit(basename(my.files2[[i]]), split = '.csv')[[1]][1]
+if (WorF == 'p') {
+pattern3="baseline1|baseline2|AMPA|CNQX|NMDA|DAP5"
+DIV=regmatches(basename(my.files2[[i]]), regexpr(pattern3, basename(my.files2[[i]])))
+DIV=paste0('DIV',DIV)
+}
+pattern2="N\\d{3,}"
+plateN=regmatches(basename(my.files2[[i]]), regexpr(pattern2,basename(my.files2[[i]])))
+# CHECKTHIS THING!!!ExpDate="210226"
+#=regmatches(basename(my.files2[[i]]), regexpr('\\d{5,}', basename(my.files2[[i]])))
+export_name <- paste0(my.input2, '/',plateN, '_', ExpDate, '_', ExpName,'_', DIV, '_', 'spikes', '_', my.well_number, '.csv')
+#export_name <- paste0(my.input2, '/',new.basename, '_', my.well_number, '.csv')
+write.csv(new.df, file = export_name, row.names = FALSE, quote = FALSE)
+}