Can R Markdown display ggplot graphs created within a function? - r

Question

I have a function called "my function" which creates a ggplot graph and saves it within the function.
#define a function "add_data" to transpose peak values into summary table
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.jpg"), width = 8, height = 4)
# Return
return(summarypeaks)
}
When I knit the document, the ggplot graph doesn't show in my HTML output despite these parameters
{r fig.cap="Experiment DATE", results = TRUE, eval = TRUE, echo= FALSE, warning=FALSE, message=FALSE, error=FALSE}
#Add experiment and condition
summarypeaks <- my_function(1284, "CONDITION")
Is there a way for the R Markdown HTML document to display the outputs of plots created within a function?

Answer 1

There's a way of getting the plot to show even without returning it, by using side effects. Specifically, you need to save your ggplot object into some variable, say p, and then tell R to print it using plot(). You don't need to change anything about how your function returns its results, it will just happen as a side effect. See below an updated version of your function:
#define a function "add_data" to transpose peak values into summary table
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
p <- 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())
plot(p)
#####SAVE GRAPH#####
#Save line graph as .png file
ggsave(filename = paste0(exp, "_Line_Graph.jpg"), width = 8, height = 4)
# Return
return(summarypeaks)
}