Looping through variables to make many boxplots - r

Question

I am using from the package OlinkAnalyze and I am trying to make box plots.
install.packages("OlinkAnalyze")
library(OlinkAnalyze)
df = npx_data1
the code for the boxplot is:
plot <- df %>%
na.omit() %>% # removing missing values which exists for Site
olink_boxplot(variable = "Site",
olinkid_list = c("OID01216", "OID01217"),
number_of_proteins_per_plot = 2)
plot[[1]]
It takes values from the olinkID column. What I would like, is to loop through the column, choosing the next two olinkID at a time, to make boxplots, renaming the plot each time (e.g.plot 1 with OID01216 and OID01217 and plot 2 with OID01218 OID01219

Answer 1

I used a while loop.
install.packages("OlinkAnalyze")
library(OlinkAnalyze)
df = npx_data1
i <- 1
ids <- as.data.frame(unique(df$OlinkID))
while(i <= nrow(ids)){
print(i)
x <- i+1
temp <- ids[i:x,]
plotx <- df %>%
na.omit() %>% #
olink_boxplot(variable = "Site",
olinkid_list = c(paste(c(ids[i,],ids[x,]))),
number_of_proteins_per_plot = 2)
plottemp <- assign(paste0("plot_",ids[i,],"_",ids[i,]),plotx)
i <- i+2
}

Answer 2

If you want the loop, you could write like this:
for i in seq(from = 1, to = length(data$OlinkID), by = 2){
the plot code
}
This way you can access the two observations you want by data$OlinkID[i] or data$OlinkID[i+1].
So the boxplot code should be
plot <- data %>%
na.omit() %>%
olink_boxplot(variable = "Oxwatchtime",
olinkid_list = c(data$OlinkID[i],data$OlinkID[i+1]),
number_of_proteins_per_plot = 2)
If you want to save the plots, add a ggsave() or a png()/pdf() in the loop to save them externally or create a list with them using ggarrange() function from ggpubr package. Let me know if it works as you intended.

Answer 3

OlinkAnalyze::olink_boxplot() plots several plots until all proteins specified under the olinkid_list argument are plotted. The number_of_proteins_per_plot argument determines the number of IDs plotted on one plot.
Try this:
library(OlinkAnalyze)
data("npx_data1")
ids <- unique(npx_data1$OlinkID)
olink_boxplot(npx_data1,
variable = "Site",
olinkid_list = ids,
verbose = TRUE,
number_of_proteins_per_plot = 2)
The code runs for a while as each plot takes time to be generated. When it completes you can use the arrow buttons in RStudio to look at all the plots.