drmowinckels
commented
4 years ago Hi!
Yes, thanks for this. It seems I have managed to unsync ggsegExtra from a large change we did in ggseg and ggseg3d last week (i did not push changes to master branch).
I will get this sorted today, hopefully, but for now you should be able to have a work-around untill I do get it fixed by renaming the area column in the atlas to region.
You can inspect the atlas' data by just typing the atlas name in the R console. The data is lazy-loaded, like many other datasets in R (like iris and mtcars).
library(ggseg)
#> Loading required package: ggplot2
library(ggsegExtra)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
ggseg(atlas=glasser)
#> Warning in ggseg(atlas = glasser): This is not a ggseg_atlas-class. Attempting
#> to convert with `as_ggseg_atlas()`
#> Error in as_ggseg_atlas(geobrain): There are missing necessary columns in the data.frame for it to be a ggseg_atlas: 'region'
ggseg(atlas = rename(glasser, region=area))
glasser
#> # A tibble: 385 x 6
#> atlas area hemi side label ggseg
#> <chr> <chr> <chr> <chr> <chr> <list>
#> 1 glasser 1 left lateral L_1_ROI <tibble [74 × 4]>
#> 2 glasser 1 left medial L_1_ROI <tibble [10 × 4]>
#> 3 glasser 1 right lateral R_1_ROI <tibble [62 × 4]>
#> 4 glasser 10d left medial L_10d_ROI <tibble [26 × 4]>
#> 5 glasser 10d right medial R_10d_ROI <tibble [26 × 4]>
#> 6 glasser 10pp left lateral L_10pp_ROI <tibble [41 × 4]>
#> 7 glasser 10pp right medial R_10pp_ROI <tibble [12 × 4]>
#> 8 glasser 10r left medial L_10r_ROI <tibble [34 × 4]>
#> 9 glasser 10r right medial R_10r_ROI <tibble [33 × 4]>
#> 10 glasser 10v left medial L_10v_ROI <tibble [43 × 4]>
#> # … with 375 more rows
rename(glasser, region=area)
#> # A tibble: 385 x 6
#> atlas region hemi side label ggseg
#> <chr> <chr> <chr> <chr> <chr> <list>
#> 1 glasser 1 left lateral L_1_ROI <tibble [74 × 4]>
#> 2 glasser 1 left medial L_1_ROI <tibble [10 × 4]>
#> 3 glasser 1 right lateral R_1_ROI <tibble [62 × 4]>
#> 4 glasser 10d left medial L_10d_ROI <tibble [26 × 4]>
#> 5 glasser 10d right medial R_10d_ROI <tibble [26 × 4]>
#> 6 glasser 10pp left lateral L_10pp_ROI <tibble [41 × 4]>
#> 7 glasser 10pp right medial R_10pp_ROI <tibble [12 × 4]>
#> 8 glasser 10r left medial L_10r_ROI <tibble [34 × 4]>
#> 9 glasser 10r right medial R_10r_ROI <tibble [33 × 4]>
#> 10 glasser 10v left medial L_10v_ROI <tibble [43 × 4]>
#> # … with 375 more rowsCreated on 2020-03-18 by the reprex package (v0.3.0)
Despiste install of ggseg and ggsegExtra finishing fine and loading fine there seems to be an issue with loading any of the additional atlasess:
Aside from that I was wondering where I can access the file naming list for each atlas?