matlab - how to make a topoplot in R with coordinates variable distribution

I would like to adapt the example I have found in this page and readapt it to my data in order to get the final topoplot realized with ggplot2

topoplot in ggplot2 – 2D visualisation of e.g. EEG data

Unfortunately it seems I having some problem with the interpolation system. Indeed when I try to plot the coordinates, they have spatial distribution very different from what they are supposed to be (my case is on the right and there is a different scale too)

This creates a problem to make work the interpolation example posted there. I tried to find some workaround and I used a different system with another package, called MBA

dat_interp <- mba.surf(cbind(dat$x, dat$y, dat$signal), no.X = 1000, no.Y = 1000)$xyz.est
mba_result <- MBA::mba.surf(cbind(dat$x, dat$y, dat$signal), 
                            no.X = 1000, no.Y = 1000)

dat_interp_df <- expand.grid(x = dat_interp$x, y = dat_interp$y)
dat_interp_df$signal <- as.vector(dat_interp$z)
ggplot() +
  geom_tile(data = dat_interp_df, aes(x = x, y = y, fill = signal)) +
  geom_point(data = dat, aes(x = x, y = y, color = signal),
             shape = 21, colour = 'black', fill = 'white', size = 2) +
  scale_fill_viridis_c() +
  scale_color_viridis_c() +
  ggtitle("Topography") +
  theme_void()

which is a result far away from what I would liek to recreate. Is there anyone that can help me with this out. Here as follows my data:

dput(dat)
structure(list(X = 1:64, label = c("AF3", "AF4", "AF7", "AF8", 
"AFz", "C1", "C2", "C3", "C4", "C5", "C6", "CP1", "CP2", "CP3", 
"CP4", "CP5", "CP6", "CPz", "Cz", "F1", "F2", "F3", "F4", "F5", 
"F6", "F7", "F8", "FC1", "FC2", "FC3", "FC4", "FC5", "FC6", "FCz", 
"FT7", "FT8", "Fp1", "Fp2", "Fpz", "Fz", "Iz", "O1", "O2", "Oz", 
"P1", "P10", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", 
"PO3", "PO4", "PO7", "PO8", "POz", "Pz", "T7", "T8", "TP7", "TP8"
), x = c(-33.706, 35.738, -54.873, 55.806, 0.23117, -36.269, 
37.675, -65.418, 67.104, -80.273, 83.413, -35.631, 38.16, -64.113, 
66.3, -79.863, 83.134, 0, 0.47908, -27.501, 29.475, -50.221, 
51.912, -64.49, 67.878, -70.233, 73.024, -34.049, 34.793, -60.191, 
62.341, -77.199, 79.561, 0.37692, -80.826, 81.786, -29.391, 29.902, 
0.11233, 0.31257, 0, -30.195, 29.937, 0, -29.247, 74.343, 32.545, 
-53, 55.408, -66.98, 68.381, -72.811, 72.81, -73.635, -36.844, 
36.608, -54.282, 55.984, 0, 0, -84.117, 85.068, -85.242, 85.591
), y = c(76.785, 77.701, 68.493, 69.657, 80.761, -9.7183, -9.3934, 
-11.535, -10.868, -13.721, -12.764, -47.284, -47.123, -46.581, 
-46.424, -46.109, -46.082, -47.183, -9.1413, 56.889, 57.599, 
53.107, 54.323, 48.069, 49.861, 42.535, 44.399, 26.032, 26.41, 
22.744, 23.681, 18.676, 19.984, 27.439, 14.106, 15.454, 83.929, 
84.91, 88.283, 58.525, -118.78, -112.69, -111.73, -115.07, -80.356, 
-74.343, -80.553, -78.576, -79.131, -77.052, -75.945, -72.811, 
-72.81, -73.635, -101.23, -100.58, -97.927, -96.966, -102.2, 
-81.305, -16.351, -15, -45.324, -45.51), signal = c(0.356912525947854, 
0.441154040587387, 0.127495728211593, 0.209844264592143, 0.471423541381149, 
0.920244846231276, 1.20067778812602, 0.901957655651085, 1.26828922845346, 
0.913597538349512, 0.961279110570437, 1.70669913750882, 1.71209354564514, 
1.54924715577636, 1.69030506815152, 1.57151232049429, 1.52222537801321, 
1.7682950526965, 1.00052912202385, 0.258051875687978, 0.473055705981418, 
0.281706344592271, 0.425239318349764, 0.391951492462168, 0.265733842589671, 
0.207140129446265, 0.237923276586573, 0.284985208364728, 0.587702684164806, 
0.337358918978001, 0.722237508242702, 0.532691597382293, 0.613087103723537, 
0.395202773422108, 0.719928099089211, 0.256588947956852, 0.433203966266369, 
0.360419814621179, 0.490884077829908, 0.391080737042044, 0.494551323229936, 
1.33255331306293, 1.1550019409092, 0.943146310863848, 2.13507543110418, 
0.605380856482758, 2.05759696362809, 2.16419480467961, 1.95371325977124, 
1.99675377322271, 1.67495247573419, 1.64695492742097, 1.33445815225302, 
0.772128251322973, 2.07429881383391, 1.60452882592484, 1.53601914533575, 
1.38352896104063, 1.83063042527717, 2.17298717559065, 0.841149491013589, 
0.443649019354451, 1.28666049614812, 0.982024863842714)), row.names = c(NA, 
-64L), class = c("tbl_df", "tbl", "data.frame"))

I would like to adapt the example I have found in this page and readapt it to my data in order to get the final topoplot realized with ggplot2

topoplot in ggplot2 – 2D visualisation of e.g. EEG data

This creates a problem to make work the interpolation example posted there. I tried to find some workaround and I used a different system with another package, called MBA

dat_interp <- mba.surf(cbind(dat$x, dat$y, dat$signal), no.X = 1000, no.Y = 1000)$xyz.est
mba_result <- MBA::mba.surf(cbind(dat$x, dat$y, dat$signal), 
                            no.X = 1000, no.Y = 1000)

dat_interp_df <- expand.grid(x = dat_interp$x, y = dat_interp$y)
dat_interp_df$signal <- as.vector(dat_interp$z)
ggplot() +
  geom_tile(data = dat_interp_df, aes(x = x, y = y, fill = signal)) +
  geom_point(data = dat, aes(x = x, y = y, color = signal),
             shape = 21, colour = 'black', fill = 'white', size = 2) +
  scale_fill_viridis_c() +
  scale_color_viridis_c() +
  ggtitle("Topography") +
  theme_void()

which is a result far away from what I would liek to recreate. Is there anyone that can help me with this out. Here as follows my data:

dput(dat)
structure(list(X = 1:64, label = c("AF3", "AF4", "AF7", "AF8", 
"AFz", "C1", "C2", "C3", "C4", "C5", "C6", "CP1", "CP2", "CP3", 
"CP4", "CP5", "CP6", "CPz", "Cz", "F1", "F2", "F3", "F4", "F5", 
"F6", "F7", "F8", "FC1", "FC2", "FC3", "FC4", "FC5", "FC6", "FCz", 
"FT7", "FT8", "Fp1", "Fp2", "Fpz", "Fz", "Iz", "O1", "O2", "Oz", 
"P1", "P10", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", 
"PO3", "PO4", "PO7", "PO8", "POz", "Pz", "T7", "T8", "TP7", "TP8"
), x = c(-33.706, 35.738, -54.873, 55.806, 0.23117, -36.269, 
37.675, -65.418, 67.104, -80.273, 83.413, -35.631, 38.16, -64.113, 
66.3, -79.863, 83.134, 0, 0.47908, -27.501, 29.475, -50.221, 
51.912, -64.49, 67.878, -70.233, 73.024, -34.049, 34.793, -60.191, 
62.341, -77.199, 79.561, 0.37692, -80.826, 81.786, -29.391, 29.902, 
0.11233, 0.31257, 0, -30.195, 29.937, 0, -29.247, 74.343, 32.545, 
-53, 55.408, -66.98, 68.381, -72.811, 72.81, -73.635, -36.844, 
36.608, -54.282, 55.984, 0, 0, -84.117, 85.068, -85.242, 85.591
), y = c(76.785, 77.701, 68.493, 69.657, 80.761, -9.7183, -9.3934, 
-11.535, -10.868, -13.721, -12.764, -47.284, -47.123, -46.581, 
-46.424, -46.109, -46.082, -47.183, -9.1413, 56.889, 57.599, 
53.107, 54.323, 48.069, 49.861, 42.535, 44.399, 26.032, 26.41, 
22.744, 23.681, 18.676, 19.984, 27.439, 14.106, 15.454, 83.929, 
84.91, 88.283, 58.525, -118.78, -112.69, -111.73, -115.07, -80.356, 
-74.343, -80.553, -78.576, -79.131, -77.052, -75.945, -72.811, 
-72.81, -73.635, -101.23, -100.58, -97.927, -96.966, -102.2, 
-81.305, -16.351, -15, -45.324, -45.51), signal = c(0.356912525947854, 
0.441154040587387, 0.127495728211593, 0.209844264592143, 0.471423541381149, 
0.920244846231276, 1.20067778812602, 0.901957655651085, 1.26828922845346, 
0.913597538349512, 0.961279110570437, 1.70669913750882, 1.71209354564514, 
1.54924715577636, 1.69030506815152, 1.57151232049429, 1.52222537801321, 
1.7682950526965, 1.00052912202385, 0.258051875687978, 0.473055705981418, 
0.281706344592271, 0.425239318349764, 0.391951492462168, 0.265733842589671, 
0.207140129446265, 0.237923276586573, 0.284985208364728, 0.587702684164806, 
0.337358918978001, 0.722237508242702, 0.532691597382293, 0.613087103723537, 
0.395202773422108, 0.719928099089211, 0.256588947956852, 0.433203966266369, 
0.360419814621179, 0.490884077829908, 0.391080737042044, 0.494551323229936, 
1.33255331306293, 1.1550019409092, 0.943146310863848, 2.13507543110418, 
0.605380856482758, 2.05759696362809, 2.16419480467961, 1.95371325977124, 
1.99675377322271, 1.67495247573419, 1.64695492742097, 1.33445815225302, 
0.772128251322973, 2.07429881383391, 1.60452882592484, 1.53601914533575, 
1.38352896104063, 1.83063042527717, 2.17298717559065, 0.841149491013589, 
0.443649019354451, 1.28666049614812, 0.982024863842714)), row.names = c(NA, 
-64L), class = c("tbl_df", "tbl", "data.frame"))

Share Improve this question asked yesterday 12666727b9 1,1392 gold badges11 silver badges26 bronze badges

1 Can you explain what is wrong with the plot you have created? I mean, obviously it is stretched out horizontally, but you could easily fix this by altering the aspect ratio. – Allan Cameron Commented yesterday
It should look like the one you could find down the website whose I left the link in the post. There are subtle within areas colored in white (clusters), the shape of circle around that plus the nose (triangle) on the top. The background should be white too. You can check through that webpsge via link. – 12666727b9 Commented yesterday

Add a comment |

1 Answer 1

Sorted by: Reset to default 1

You can mask your interpolation grid with an ellipse and draw a nose polygon. I also added some white contour lines. Note, that if we use this masked approach, we need to extend the bounds of mba.surf in bbox. I added theme_bw() for the white background and coord_fixed() to retain the axis-ratio provided in data.

library(MBA)
library(ggplot2)

# Nose
hr <- min(max(abs(dat$x)), max(abs(dat$y))) *1.1
nose_df <- data.frame(x = c(-0.1, 0, 0.1) * hr, 
                      y = c(0.98, 1.1, 0.98) * hr) # maybe adjust thes triangle points!

# head ellipse
theta <- seq(0, 2*pi, length.out = 100)
a <- hr * 0.97   # horizontal radius
b <- hr * 1.15   # vertical radius
y_offset <- 15
head_df <- data.frame(x = a * cos(theta), y = b * sin(theta) - y_offset)

dat_interp <- mba.surf(cbind(dat$x, dat$y, dat$signal), 
                       no.X = 1000, 
                       no.Y = 1000,
                       extend = TRUE, 
                       b.box=c(min(dat$x)-20, max(dat$x)+20, min(dat$y)-20, max(dat$y)+20) # I extended the grid a little
                       )$xyz.est
mba_result <- MBA::mba.surf(cbind(dat$x, dat$y, dat$signal), 
                            no.X = 1000, no.Y = 1000,
                            extend = TRUE)
dat_interp_df <- expand.grid(x = dat_interp$x, y = dat_interp$y)
dat_interp_df$signal <- as.vector(dat_interp$z)

# Create mask for ellipse
dat_interp_df <- dat_interp_df[((dat_interp_df$x / a)^2 + ((dat_interp_df$y + y_offset) / b)^2) <= 1, ]

# plot
ggplot() +
  geom_tile(data = dat_interp_df, aes(x = x, y = y, fill = signal)) +
  geom_contour(data = dat_interp_df, aes(x = x, y = y, z = signal), colour = 'white', alpha = 0.5) +
  geom_point(data = dat, aes(x = x, y = y, color = signal),
             shape = 21, colour = 'black', fill = 'white', size = 2) +
  geom_path(data = head_df, aes(x = x, y = y), color = "black", size = 0.5) + # head
  geom_polygon(data = nose_df, aes(x = x, y = y), fill = "white", colour = 'black') + # nose
  ggtitle("Topography") +
  scale_fill_viridis_c() +
  scale_color_viridis_c() +
  theme_bw() +
  coord_fixed()

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matlab - how to make a topoplot in R with coordinates variable distribution - Stack Overflow

1 Answer 1

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