Using scatterbar with Visium data

Below is how to use scatterbar from the provided Visium dataset of an FFPE preserved adult mouse brain partial coronal section from 10X Genomics.

library(scatterbar)
library(ggplot2)
data("adult_mouse_brain_ffpe")

plot(adult_mouse_brain_ffpe$pos)

head(adult_mouse_brain_ffpe$prop)
#>                            1          2         3         4         5         6
#> AAACAGAGCGACTCCT-1 0.1264103 0.00000000 0.0000000 0.2183626 0.0000000 0.0000000
#> AAACCCGAACGAAATC-1 0.0000000 0.00000000 0.0000000 0.0000000 0.1612265 0.7494948
#> AAACCGGGTAGGTACC-1 0.2881994 0.32242398 0.0000000 0.3893766 0.0000000 0.0000000
#> AAACCGTTCGTCCAGG-1 0.3040547 0.27785934 0.2535515 0.0000000 0.0000000 0.0000000
#> AAACGAAGAACATACC-1 0.1585737 0.09403518 0.0000000 0.3510139 0.0000000 0.0000000
#> AAACGAGACGGTTGAT-1 0.0000000 0.00000000 0.2962469 0.0000000 0.0000000 0.0000000
#>                            7 8          9 10         11         12
#> AAACAGAGCGACTCCT-1 0.1865617 0 0.07496736  0 0.39369799 0.00000000
#> AAACCCGAACGAAATC-1 0.0000000 0 0.00000000  0 0.00000000 0.08927876
#> AAACCGGGTAGGTACC-1 0.0000000 0 0.00000000  0 0.00000000 0.00000000
#> AAACCGTTCGTCCAGG-1 0.0768548 0 0.00000000  0 0.08767969 0.00000000
#> AAACGAAGAACATACC-1 0.2808292 0 0.00000000  0 0.11554800 0.00000000
#> AAACGAGACGGTTGAT-1 0.0000000 0 0.00000000  0 0.00000000 0.70375311

start.time <- Sys.time()
scatterbar(
  adult_mouse_brain_ffpe$prop,
  adult_mouse_brain_ffpe$pos,
  size_x = 220,
  size_y = 220,
  legend_title = "Cell Types"
) + coord_fixed()


end.time <- Sys.time()
print(end.time - start.time)
#> Time difference of 0.5269275 secs

Just like with the mOB data, we can change the order of how each bar is laid out by changing the order of the cell-type proportion matrix and combine scatterbar with other ggplot geoms and customization.

start.time <- Sys.time()
custom_colors <- c('1'= '#5d6f99',
    '2' = '#985a39',
    '3' =  '#d6589a',
    '4' = '#4d1395',
    '5' = '#b5ef27',
    '6' = '#77d5bc',
    '7' = '#7830d2',
    '8' ='#b43b59',
    '9' = '#1c40b1',
    '10' = "#FF5733",
    '11' = '#FFFF00',
    '12' = '#f4a6f1')
scatterbar::scatterbar(adult_mouse_brain_ffpe$prop[, c(2,3,4,11,5,6,10,7,8,1,9, 12)], adult_mouse_brain_ffpe$pos, size_x = 220, size_y = 220, padding_x = 0.1, padding_y = 0.1, legend_title = 'Cell Type', colors = custom_colors) +
  geom_point(data=adult_mouse_brain_ffpe$pos, mapping=aes(x=x, y=y), size = 0.1) +
  theme_bw() + ylab('y') + ggplot2::coord_fixed()

end.time <- Sys.time()
print(end.time - start.time)
#> Time difference of 0.4268332 secs

Using scatterbar with Visium data

Jean Fan and Dee Velazquez

2024-10-18

Using scatterbar with Visium data