CODEWITHSUNDEEP
rplot
Yilun Zhang
Yilun Zhang

Reputation: 9018

R plot based on another factor

I have a set of data looks like this:

CHROM POS GT DIFF

chr01 integer AG integer

chr01 integer GA integer

chr02 integer CG integer

..

chr22 integer GT integer

chrX integer TC integer

I want to plot POS(x-axis) vs DIFF(y-axis), and I want to group x-axis based on the level of CHROM.

Below is a sample plot I have only for chr01. I want to have chr02 ... chrX in this plot as well to the right of chr01.

My code is:

my.key <- list(space="right",
           border=T,
           cex.title=1.2,
           title="Legend",
           size=10,
           text=levels(GT),
           fill=T)

xyplot(data$DIFF[data$CHROM=="chr01"]~data$POS[data$CHROM=="chr01"],
   xlab = "chr01 -- LCMT0001",
   ylab = "Distance -- LCMT0001",
   col=GT,
   group=GT,
   auto.key = my.key,
   pch=16,
   scales=list(
     x = list(alternating=F,tick.number = 8),
     y = list(log=10,tick.number=11))

)

Upvotes: 0

Views: 72

Answers (1)

Henrik
Henrik

Reputation: 67778

You may try ggplot:

# some sample data
df <- data.frame(CHROM = 1:4,
                 POS = 1:5,
                 GT = sample(c("ac", "ag", "at"), 100, replace = TRUE),
                 DIFF= sample(1:100))


ggplot(data = df, aes(x = POS, y = DIFF, colour = GT)) +
  geom_point() +
  facet_grid(~ CHROM) +
  theme_bw()

enter image description here

Upvotes: 1

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