This notebook describes a data analysis done on Arabidopsis experiment, performed by Katie Carson at BTI in July 2024, during her REU program.
The data was subsequently analyzed using CropReporter software and wrangled by Magda Julkowska.
list.files(pattern = "txt")
[1] "Katie_Tray01.txt" "Katie_Tray02.txt" "Katie_Tray03.txt" "Katie_Tray04.txt" "Katie_Tray05.txt" "Katie_Tray06.txt" "Katie_Tray07.txt" "Katie_Tray08.txt" "Katie_Tray09.txt" "Katie_Tray10.txt"
[11] "Katie_Tray11.txt" "Katie_Tray12.txt" "Katie_Tray13.txt" "Katie_Tray14.txt" "new_file.txt"
Katie <- read.table("Katie_Tray01.txt", header = TRUE, sep = "\t")
Warning in read.table("Katie_Tray01.txt", header = TRUE, sep = "\t") :
incomplete final line found by readTableHeader on 'Katie_Tray01.txt'
Katie
Let’s remove all of the lines where our ROI (Region of Interest) is “All” instead of the selected Pots for Arabidopsis:
Katie <- Katie[Katie$Roi.No != "All", ]
Katie
All right - now let’s keep only the measurements that are meaningful for now:
colnames(Katie)