plot rectangles with gg polygon R

Question

I want to draw a series of rectangles on a plot in ggplot, depicting regions of a protein. The basic data looks like:

x    y     ids
6   9851    IgLike
10216   12022   PEVK
12041   14012   IgLike
14019   32144   Fibronectin
32178   32432   ProteinKinase
32496   34344   IgLike

Column one to column two indicates the region across the x axis i want labelled as column 3. I tried to follow the guide at http://docs.ggplot2.org/current/geom_polygon.html by Hadley, but it's a tad confusing. I have the data transformed to "positions" ;

9851    .75  IgLike
6   0.75    IgLike
6   .9  IgLike
9851    .9  IgLike

12022   .75 PEVK
10216   0.75    PEVK
 10216  .9  PEVK
12022   .9  PEVK

14012   .75 IgLike
12041   0.75    IgLike
12041   .9  IgLike
14012   .9  IgLike

32144   .75 Fibronectin
14019   0.75    Fibronectin
14019   .9  Fibronectin
32144   .9  Fibronectin

32432   .75 ProteinKinase
32178   0.75    ProteinKinase
32178   .9  ProteinKinase
32432   .9  ProteinKinase

34344   .75 IgLike
32496   0.75    IgLike
32496   .9  IgLike
34344   .9  IgLike

which is almost there, but some of the shapes are overlapping, instead of being discrete shapes as they should be. The y axis values of .75 and .9 are arbitrary, I just want some thickness so its readily visible as more than just a line

then

ggplot(positions, aes(x=x, y=y)) + geom_polygon(aes(fill=ids))

Answer 1

As you only want rectangles, geom_polygon might be a little overkill. When I use your original data

df1 <- read.table(text="
                  x    y     ids
6   9851    IgLike
10216   12022   PEVK
12041   14012   IgLike
14019   32144   Fibronectin
32178   32432   ProteinKinase
32496   34344   IgLike",header=T)

I can plot it as rectangles as you already gave xmin (x) and xmax(y) on one line; the ymin and ymax variables are arbitrary.

p1 <- ggplot(df1) +
  geom_rect(aes(xmin=x,xmax=y,ymin=1,ymax=2,fill=ids))
p1