How to index coordinate data according to a grid in R?

Question

I have coordinate data (x-coordinates and y-coordinates) on a scale between: Xpos: 27-1367nm, Ypos: 67-1014nm. A data set consists of about 2500-3500 data points. Here is the header of such a data set:

   XPos YPos
1    29  211
2    31  609
3    33 1001
4    35  508
5    37  424
6    39  584
7    40  378
8    41  204
9    41  444
10   41  872 
...

[![Data plotted][1]][1]

Now I would like to index the data points by applying a grid consisting of equal sized quadrants onto the data in R. The result should be a new column "grid_index" containing a unique quadrant_ID in which the data points are located (see image). Is there an easy way to do this? I would like to try different grid unit sizes to partition the data e.g. quadrants sized 50nm, 100nm, 200nm or 400nm and rectangles sized 100nm x 200nm or 50nm x100nm.

[![Grid for data pint indexing][2]][2]

[![Each grid quadrant should have an unique ID][3]][3]

I would be very grateful for any help.

user_13095326 · Answer

Here's an approach with findInterval:

First set up a matrix that has the appropriate number of indices:

pos.matrix <- matrix(1:35,byrow = TRUE, nrow = 5)
pos.matrix
     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]    1    2    3    4    5    6    7
[2,]    8    9   10   11   12   13   14
[3,]   15   16   17   18   19   20   21
[4,]   22   23   24   25   26   27   28
[5,]   29   30   31   32   33   34   35

Next use findInterval to find the indices of the matrix of where it lies. You can control the size of the grid using the by = argument. Note that the dimensions of the matrix must match the number of intervals provided in findInterval. We need to use abs because the y values are decreasing on the graph.

grid <- apply(cbind(findInterval(data[,"XPos"],seq(0,1400,by = 200)),
                    abs(findInterval(data[,"YPos"],seq(0,1000,by = 200)) - 6)),
              MARGIN = 1,
              function(x) pos.matrix[x[2],x[1]])
grid[1:25]
[1] 30 34 31 17 19 26 15 31 19  5 18 32 25 25 14 20 22 19 35  2 16  8 29 29 16
plot(NA,xlim = c(0,1400), ylim = c(0,1000), xlab = "XPos", ylab = "YPos", cex.axis = 0.8)
text(data[,1],data[,2], labels = grid, cex = 0.4)

Sample Data

set.seed(3)
data <- data.frame(XPos = runif(1000,0,1400), YPos = runif(1000,0,1000))

How to index coordinate data according to a grid in R?

1 Answers