Discrete

If you wish to specify a default, discrete colour scale such as that produced by scale_colour_brewer() use the ggplot2.discrete.colour option. Similarly, use the option ggplot2.discrete.fill for a discrete fill scale.

Default Discrete Scales

library(ggplot2)

ggplot(mtcars, aes(hp, mpg, color = factor(cyl), fill = factor(cyl))) + geom_point()

^{Created on 2021-07-01 by the reprex package (v1.0.0)}

Custom Discrete Scales

library(ggplot2)

scale_colour_brewer_d <- function(..., palette = "Dark2") {
  scale_colour_brewer(..., palette = palette )
}

scale_fill_brewer_d <- function(..., palette = "Dark2") {
  scale_fill_brewer(..., palette = palette)
}

options(
  ggplot2.discrete.colour = scale_colour_brewer_d,
  ggplot2.discrete.fill = scale_fill_brewer_d
)

ggplot(mtcars, aes(hp, mpg, color = factor(cyl), fill = factor(cyl))) + geom_point()

^{Created on 2021-07-01 by the reprex package (v1.0.0)}

Continuous

If you wish to specify a default, continuous color scale, you will need to use scale_colour_distiller() instead of scale_colour_brewer(). Similarly, use scale_fill_distiller() as opposed to scale_fill_brewer() for a continuous fill scale. You will also use the options ggplot2.continuous.colour and ggplot2.continuous.fill respectively.

Default Continuous Scales

library(ggplot2)

ggplot(mtcars, aes(hp, mpg, color = cyl, fill = cyl)) + geom_point()

^{Created on 2021-07-01 by the reprex package (v1.0.0)}

Custom Continuous Scales

library(ggplot2)

scale_colour_brewer_c <- function(..., palette = "Dark2") {
  scale_colour_distiller(..., palette = palette )
}

scale_fill_brewer_c <- function(..., palette = "Dark2") {
  scale_fill_distiller(..., palette = palette)
}

options(
  ggplot2.continuous.colour = scale_colour_brewer_c,
  ggplot2.continuous.fill = scale_fill_brewer_c
)

ggplot(mtcars, aes(hp, mpg, color = cyl, fill = cyl)) + geom_point()

^{Created on 2021-07-01 by the reprex package (v1.0.0)}

This is because you are using scale_fill_brewer(). This command expects an RColorBrewer palette name. (e.g. "Oranges"). It cannot read your custom palette name my_palette Instead, use scale_fill_manual()

I created an own reproducible example:

library(RColorBrewer)
library(ggplot)

set.seed(1234)
df <- data.frame(x=runif(10,0,1), y=runif(10,0,1), c=factor(sample(1:5,10,replace=T)))

ggplot(data=df, aes(x=x,y=y)) + geom_point(aes(color=c)) + scale_color_brewer(palette = 'Oranges')

As you can see, I am calling the RColorBrewer palette "Oranges". As you mentioned, these coloured are very light, and you may want to use only the darker ones. To do this, you can make a custom palette and call it using scale_color_manual() (or scale_fill_manual() in your case) instead of scale_color_brewer().

my_palette <- brewer.pal(name="Oranges",n=9)[4:9]

ggplot(data=df, aes(x=x,y=y)) + geom_point(aes(color=c)) + scale_color_manual(values = my_palette)

This will now use the colors you specified in my_palette