how to control transparency of ppp density plot

Question

I am trying to use the layered methods to overlay few spatstat spatial objects. All these objects are for the same window. I have an im layer (density) from a ppp. I want to make this layer a bit transparent in order to have a better visibility of the other objects in the layered object.

How can I control the transparency of this density plot (im)? Is there something like alpha or transparency parameter for the plot.im ?

UPDATE:

library(spatstat)
pipes=simplenet
plot(pipes)
point_net = as.ppp(runifpoint(10, win = Window(pipes)))
point_surface = density(point_net)
plot(point_surface)
layers= layered(point_surface, point_net, pipes)
plot(layers)

Here , I have plotted 3 layers. As you can see the density plot has very dark blues and reds. Yes, I can plot lines and points with different colours to make them visible, but it would nice to do simple stacked line, point plots and add a little bit of transparency to the density (im) plots.

The purpose is just to avoid complex customized plot colours and to explain to colleagues.

thank you.

Please provide example code, so we can easily try to modify it to add transparency. — Ege Rubak

Ege Rubak Ege Rubak · Accepted Answer · 2017-07-29T22:38:07

First the commands from the original post:

library(spatstat)
pipes=simplenet
point_net = as.ppp(runifpoint(10, win = Window(pipes)))
point_surface = density(point_net)
layers= layered(point_surface, point_net, pipes)
plot(layers)

You need to provide a different colourmap to plot.im. There are two ways you can do this:

Plot each layer individually using add = TRUE for subsequent layers and provide the colour map when you plot the im object.
Pass a list of plot arguments when you plot the layered object you have created above.

I find the first option easier for illustration, so I will do that first. The default colourmap of spatstat is the 29th Kovesi colour sequence (?Kovesi for more details on these sequences):

def_col <- Kovesi$values[[29]]
head(def_col)
#> [1] "#000C7D" "#000D7E" "#000D80" "#000E81" "#000E83" "#000E85"

To add transparency you can use to.transparent with your choice of fraction for more/less transparency:

def_col_trans <- to.transparent(def_col, fraction = 0.7)
head(def_col_trans)
#> [1] "#000C7DB3" "#000D7EB3" "#000D80B3" "#000E81B3" "#000E83B3" "#000E85B3"

Now you just need to use this as your colourmap:

plot(point_surface, col = def_col_trans)
plot(point_net, add = TRUE)
plot(pipes, add = TRUE)

To do it with the layered object you have to make a list of plot argument lists (containing NULL if you don't have additional arguments):

layer_args <- list(list(col = def_col_trans),
                   list(NULL),
                   list(NULL))
plot(layers, plotargs = layer_args)

how to control transparency of ppp density plot

1 Answers