I have a script that looks like this:
library("UpSetR")
Data<- read.table(file=file.choose(), header=T, fill = TRUE);
Data <- as.data.frame(Data);
head(Data);
GEO<- colnames(Data);
upset(Data, sets = GEO, nsets = 6);
Data looks like this:
'data.frame': 6228 obs. of 6 variables:
$ GSE144725_CHD10: Factor w/ 6228 levels "1-Mar","11-Sep",..: 1766 3229 5321 3234 3776 1026 5001 4706 4752 5349 ...
$ GSE115310_C9 : Factor w/ 333 levels "ABHD13","ACAT2",..: 1 2 3 4 5 6 7 8 9 10 ...
$ GSE115310_sALS : Factor w/ 283 levels "AASDHPPT","ABHD13",..: 2 5 6 13 19 23 24 28 36 45 ...
$ GSE68240_sALS : Factor w/ 1586 levels "A1BG","AAAS",..: 392 357 686 704 718 203 731 1424 737 495 ...
$ GSE28253_sALS : Factor w/ 53 levels "ANAPC4","ARMC5",..: 12 20 48 4 41 14 1 18 24 44 ...
$ GSE833_sALS : Factor w/ 78 levels "ADCY1","AKAP13",..: 32 28 66 53 9 29 69 65 37 34 ...
My error:
Error in start_col:end_col : argument of length 0
I am wanting to take Data and each column associated with Data and make a UpSet plot to find overlap. Any help would be greatly appreciated. Does Factor on each column matter?
I think your dataset is not the 0/1 formation, you could try to convert your data to 0/1 like this Data[Data > 0] <- 1.
I hope it works!