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I have the data here data. I want to plot the categorically marked point pattern using spatstat in R. I have tried doing this

x = c(3,0.5,1,0,0,0,2,2.5,5.5, 16,21,26,28,40, 47, 52, 58, 60, 65, 63, 63, 75, 77, 78, 75)
y = c(116,106,82.5,64,40,35,25,17.5,5,5,5,8,10,8, 14, 14, 10, 0, 0, 17, 20, 24, 30, 50, 116)
p <- owin(poly = cbind(x, y))
point_pattern = as.ppp(deviation_binary_category_locations_marks, p)
marks(point_pattern) <- deviation_binary_category_locations_marks[, "RPL32"]
ccc <- c("green","black")[marks(point_pattern)]
shapes = c(1,21)[marks(point_pattern)]
plot(point_pattern,which.marks="RPL32", main="Point pattern for gene RPL32")
plot(point_pattern,which.marks="RPL32",bg=ccc,pch = shapes, add=TRUE)

It results in a plot like this plot

However, the circle and the triangle are not clear without colouring I think. How can I colour the triangle so it will be more obvious to see? Or change the triangle to a coloured circle? I have tried using the code mentioned above but nothing has change.

markalex
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MK Huda
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1 Answers1

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Use argument cols to specify colours for the different types of points, and chars to specify the plotting symbols for the different types of points. You could also use cex to control the size of the plot symbols to make them more distinct.

For further information see the help file for plot.ppp.

Adrian Baddeley
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  • Thanks. I just found out about plot.ppp last night actually. This is what I have been looking for. I solve it using `plot(point_pattern,which.marks="FN1", main="Point pattern for gene FN1", chars = c("o","o"), bg = c("white", "green"),pch = 21, size = 0.75, cols = c("black", "green"))` – MK Huda Nov 05 '22 at 09:49