Is it possible to create a R function for my code? - r

Question

Is there a way to create a function for my code below? I have multiple csv files that I'm running this exact code on, but it has been tiring using this same code over and over to do the same thing (and has made my script very long). Here is my code-
#define a function "add_peaks" to transpose peak values into summary table
add_peaks <- function(df, vec, colname) {
if(colname %in% names(df)) vec <- c(df[[colname]], vec)
new_row <- max(nrow(df), length(vec))
new_df <- df[1:new_row, ,drop = FALSE]
new_df[colname] <- c(vec, rep(NA, new_row - length(vec)))
new_df[is.na(new_df)] <- 0
rownames(new_df) <- NULL
new_df
}
#####INPUT#####
#Read in appropriate experiment number
#Remove first 2 columns
#Rename first column to "mintime" and convert to minutes
#Normalize raw fluorescence values
flowdata <- read_csv("####.csv") ####CHANGE EXP NUMBER
title <- "CONDITION HERE" ####CHANGE CONDITION"
flowdata <- flowdata[, -c(1:2)] %>%
rename(mintime = 1) %>%
transform(mintime = mintime / 60)
flowdata[,-1] <- data.frame(lapply(flowdata[,-1], function(X) X/X[1]))
#Exclude values up to 5 minutes
#Determine number of peaks per cell
#Add number of peaks per cell to summary table
flowdata_cut <- flowdata[which(flowdata$mintime>=5),]
peak_info <- lapply(flowdata_cut[,-1], findpeaks, threshold=2)
numberpeak <- unlist(lapply(peak_info, nrow))
summarypeaks <- add_peaks(summarypeaks, numberpeak, title)
#Prepare data for line graph
melted <- melt(flowdata, id.vars="mintime")
#####CREATE GRAPH#####
#Plot graph
ggplot(data=melted, aes(x=mintime, y=value, group=variable)) +
geom_line(show.legend = FALSE) +
scale_x_continuous(limits = c(3, 12), breaks = seq(3, 12, by = 3)) +
labs(y="Fluo-4 fluorescence (F/F0)", x = "Time (min)") +
ggtitle(title) +
theme_bw() +
# remove elements we don't need
theme(panel.grid = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"),
panel.background = element_blank())
#####SAVE GRAPH#####
#Save line graph as .png file
ggsave(filename = "####_Line_Graph.png", ####CHANGE EXP NUMBER
width = 8, height = 4)
Please let me know if it is possible (code is appreciated), even if it is part of it only. Obviously I am new to coding. Thank you!

Answer 1

Below is your code, extracted into a function that takes 2 arguments - the experiment number (exp) and the condition (cond).
my_function <- function(exp, cond) {
#Read in appropriate experiment number
#Remove first 2 columns
#Rename first column to "mintime" and convert to minutes
#Normalize raw fluorescence values
flowdata <- read_csv(paste0(exp, ".csv"))
title <- cond
flowdata <- flowdata[, -c(1:2)] %>%
rename(mintime = 1) %>%
transform(mintime = mintime / 60)
flowdata[,-1] <- data.frame(lapply(flowdata[,-1], function(X) X/X[1]))
#Exclude values up to 5 minutes
#Determine number of peaks per cell
#Add number of peaks per cell to summary table
flowdata_cut <- flowdata[which(flowdata$mintime>=5),]
peak_info <- lapply(flowdata_cut[,-1], findpeaks, threshold=2)
numberpeak <- unlist(lapply(peak_info, nrow))
summarypeaks <- add_peaks(summarypeaks, numberpeak, title)
#Prepare data for line graph
melted <- melt(flowdata, id.vars="mintime")
#####CREATE GRAPH#####
#Plot graph
ggplot(data=melted, aes(x=mintime, y=value, group=variable)) +
geom_line(show.legend = FALSE) +
scale_x_continuous(limits = c(3, 12), breaks = seq(3, 12, by = 3)) +
labs(y="Fluo-4 fluorescence (F/F0)", x = "Time (min)") +
ggtitle(title) +
theme_bw() +
# remove elements we don't need
theme(panel.grid = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"),
panel.background = element_blank())
#####SAVE GRAPH#####
#Save line graph as .png file
ggsave(filename = paste0(exp, "_Line_Graph.png"), width = 8, height = 4)
# Return
return(summarypeaks)
}
If you have experiment number 005 and condition "test", call the function like so, assigning the result to replace the old value of summarypeaks:
summarypeaks <- my_function(005, "test")