ggplot heatmap comes up empty

Question

I have a large data file with a little over 1000 points. It is a large merged file from 23 other .csv files (called alltraj)

It is a format that looks like this:

    Track   X1        X         Y
1    Point    1 148.5000 306.83333
2    Point    2 149.8333 306.83333
3    Point    3 151.8333 307.16667
4    Point    4 152.5000 308.16667
5    Point    5 156.1667 309.16667
6    Point    6 159.1667 311.16667
7    Point    7 163.1667 311.83333
8    Point    8 166.5000 313.50000
9    Point    9 170.5000 316.16667
10   Point   10 177.1667 321.50000

where X1 is the time step, and X and Y are the positions of a fish.

I am trying to make a heatmap of the frequencies of my X vs Y trajectories using the following code:

(p <- ggplot(alltraj, aes(Y,X)) + 
    geom_tile(aes(fill = X1), colour = "white") + 
    scale_fill_gradient(low = "white",high = "steelblue"))

However, the heatmap comes up completely blank. And looks like this:

Can anyone tell my what I'm missing in my code that is making it come up blank? Thanks in advance!

EDIT: Here is a copy of the (unfortunately messy) first 50 lines of code that I am trying to run when I use head(alltraj, n=50)):

structure(list(Track = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Point", class = "factor"), 
X1 = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 
13L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 
26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 
38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 
50L, 51L), X = c(148.5, 149.8333333, 151.8333333, 152.5, 
156.1666667, 159.1666667, 163.1666667, 166.5, 170.5, 177.1666667, 
180.8333333, 183.5, 186.1666667, 191.8333333, 192.8333333, 
194.1666667, 195.8333333, 195.5, 196.8333333, 197.1666667, 
197.1666667, 197.1666667, 198.5, 198.5, 198.8333333, 198.5, 
197.5, 198.8333333, 199.5, 199.5, 199.5, 199.8333333, 200.8333333, 
199.8333333, 201.1666667, 201.8333333, 202.5, 203.1666667, 
203.1666667, 203.1666667, 204.5, 204.5, 204.5, 204.5, 204.8333333, 
203.8333333, 203.8333333, 204.8333333, 206.1666667, 206.5
), Y = c(306.8333333, 306.8333333, 307.1666667, 308.1666667, 
309.1666667, 311.1666667, 311.8333333, 313.5, 316.1666667, 
321.5, 323.8333333, 325.8333333, 326.1666667, 327.5, 332.1666667, 
338.1666667, 341.5, 346.5, 351.1666667, 355.8333333, 360.1666667, 
364.1666667, 368.5, 371.8333333, 375.1666667, 376.5, 381.8333333, 
385.8333333, 389.5, 392.8333333, 395.8333333, 400.1666667, 
405.1666667, 408.8333333, 413.5, 417.1666667, 420.8333333, 
424.8333333, 427.8333333, 429.8333333, 433.1666667, 434.5, 
435.1666667, 435.1666667, 436.8333333, 436.8333333, 437.5, 
438.8333333, 439.8333333, 440.1666667)), row.names = c(NA, 
50L), class = "data.frame")

It seems as if the scale is off in my heatmap. When I use the first 10 lines I get nicely sized points, but when I do the first 20, the points get smaller. When I do 30 they're even smaller. At 50, they're pretty much unreadable. How do I make the size of the points bigger?

Answer 1

Your code produces the following plot:

alltraj <- readr::read_table("Track   X1        X         Y
Point    1 148.5000 306.83333
Point    2 149.8333 306.83333
Point    3 151.8333 307.16667
Point    4 152.5000 308.16667
Point    5 156.1667 309.16667
Point    6 159.1667 311.16667
Point    7 163.1667 311.83333
Point    8 166.5000 313.50000
Point    9 170.5000 316.16667
Point   10 177.1667 321.50000")

library("ggplot2")

p <- ggplot(alltraj, aes(Y,X)) + 
    geom_tile(aes(fill = X1), colour = "white") + 
    scale_fill_gradient(low = "white",high = "steelblue")

p

The heatmap is not empty. This likely means your reproducible example does not actually reproduce the issue... What happens when you run the code above?

Empty plots typically happen when you forgot to add a layer (i.e. you just called ggplot but no geom_XXX). This also happens when you think you have added a layer but forgot the + sign...

For example, you'll end up with an empty plot if you run the following (note the missing + at the end of the first line):

p <- ggplot(alltraj, aes(Y,X)) 
    geom_tile(aes(fill = X1), colour = "white") + 
    scale_fill_gradient(low = "white",high = "steelblue")

Edit after investigation

Using geom_tile creates tiles at the X and Y position you specify. Is implies your X and Y are already arranged in a grid! It is not the case here, and you end up with minuscule tiles (with width the smallest dX and height the smallest dY).

The solution is to use geom_bin2d which first bins your data (i.e. creates a coarse grid) and only then plots.

On your small example, the difference is not obvious but already the tiles are bigger. You can pick the most appropriate binwidth.

ggplot(alltraj, aes(x=Y, y=X)) + 
    geom_bin2d(colour = "white", binwidth=10)

However that does mean that you can't use X1 as fill (does not make sense in a binned context). If you need to plot X1, it indicates you are using the wrong geom and a heatmap may not be appropriate. Markus suggest in the comments that you may be interested to use geom_path.