I would have to know more about RStudio internals than I do or ever will to explain the messages, so I've run code with random numeric objects in a dataframe
> x <- sort(rnorm(47))
> y <- sort(rnorm(47))
> plot(x,y)
> CHROM <- x
> Fst <- y
> GRAPHING_FST_JUZ_BLV_noUN <- as.data.frame(cbind(CHROM,Fst))
> head(GRAPHING_FST_JUZ_BLV_noUN)
CHROM Fst
1 -2.547468 -2.174413
2 -1.774497 -2.142001
3 -1.526069 -1.903299
4 -1.482865 -1.721827
5 -1.387847 -1.704770
6 -1.361492 -1.630904
> plot(GRAPHING_FST_JUZ_BLV_noUN$CHROM,GRAPHING_FST_JUZ_BLV_noUN$Fst, type = "p")
without problem.
So then, I converted the arguments to factors
> CHROM <- factor(x)
> Fst <- factor(y)
> GRAPHING_FST_JUZ_BLV_noUN <- as.data.frame(cbind(CHROM,Fst))
>
> plot(GRAPHING_FST_JUZ_BLV_noUN$CHROM,GRAPHING_FST_JUZ_BLV_noUN$Fst, type = "p")
Again, no problem.
However, treating the argument as character type reproduces your problem
> CHROM <- as.character(x)
> Fst <- as.character(y)
> GRAPHING_FST_JUZ_BLV_noUN <- as.data.frame(cbind(CHROM,Fst))
> plot(GRAPHING_FST_JUZ_BLV_noUN$CHROM,GRAPHING_FST_JUZ_BLV_noUN$Fst, type = "p")
Warning message:
In rect(xleft, ybottom, xright, ytop, col = col, ...) :
graphical parameter "type" is obsolete
So, I suspect your source data may have been in CSV form with at least one numeric column "Fst", say, in quotes.