adapted atlases to ggseg <= 1.6.0

ggseg · Nov 18, 2020 · fdf59cd · fdf59cd
1 parent a6d34c1
commit fdf59cd
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diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,4 @@
+# ggsegChen 1.0.01
+
+* adapted atlases to ggseg <= 1.6.0
+* Added a `NEWS.md` file to track changes to the package.
diff --git a/README.Rmd b/README.Rmd
@@ -10,7 +10,8 @@ knitr::opts_chunk$set(
   comment = "#>",
   fig.path = "man/figures/README-",
   fig.width = 6,
-  out.width = "100%"
+  out.width = "100%",
+  fig.retina = 3
 )
 devtools::load_all(".")
 ```
@@ -49,21 +50,18 @@ library(ggsegChen)
 ```{r}
 library(ggseg)
 
-ggseg(atlas = chenAr, mapping = aes(fill = region)) +
-  scale_fill_brain("chenAr", package = "ggsegChen") +
+plot(chenAr) +
   labs(title = "Chen areal (chenAr)") +
   theme(legend.position = "bottom",
         legend.text = element_text(size = 9)) +
   guides(fill = guide_legend(ncol = 3))
 ```
 ```{r fig.height = 6}
-ggseg(atlas = chenTh, mapping = aes(fill = region)) +
-  scale_fill_brain("chenTh", package = "ggsegChen") +
+plot(chenTh) +
   labs(title = "Chen thickness (chenTh)") +
   theme(legend.position = "bottom",
         legend.text = element_text(size = 9)) +
   guides(fill = guide_legend(ncol = 2))
-
 ```
 
 <!-- ```{r "noneval", eval=FALSE} -->

diff --git a/README.md b/README.md
@@ -46,8 +46,7 @@ library(ggsegChen)
 ``` r
 library(ggseg)
 
-ggseg(atlas = chenAr, mapping = aes(fill = region)) +
-  scale_fill_brain("chenAr", package = "ggsegChen") +
+plot(chenAr) +
   labs(title = "Chen areal (chenAr)") +
   theme(legend.position = "bottom",
         legend.text = element_text(size = 9)) +
@@ -57,8 +56,7 @@ ggseg(atlas = chenAr, mapping = aes(fill = region)) +
 <img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
 
 ``` r
-ggseg(atlas = chenTh, mapping = aes(fill = region)) +
-  scale_fill_brain("chenTh", package = "ggsegChen") +
+plot(chenTh) +
   labs(title = "Chen thickness (chenTh)") +
   theme(legend.position = "bottom",
         legend.text = element_text(size = 9)) +

diff --git a/data-raw/chen.R b/data-raw/chen.R
@@ -34,6 +34,8 @@ chenTh <- chenTh %>%
                        long - diff, long))
 
 chenTh <- as_ggseg_atlas(chenTh)
+chenTh <- as_brain_atlas(chenTh)
+chenTh$palette <- brain_pals$chenTh
 usethis::use_data(chenTh, internal = FALSE, overwrite = TRUE, compress = "xz")
 
 
@@ -71,6 +73,8 @@ chenAr <- chenAr %>%
                        long - diff, long))
 
 chenAr <- as_ggseg_atlas(chenAr)
+chenAr <- as_brain_atlas(chenAr)
+chenAr$palette <- brain_pals$chenAr
 usethis::use_data(chenAr, internal = FALSE, overwrite = TRUE, compress = "xz")
 
 

diff --git a/data/chenAr.rda b/data/chenAr.rda
diff --git a/data/chenTh.rda b/data/chenTh.rda
diff --git a/man/figures/README-unnamed-chunk-3-1.png b/man/figures/README-unnamed-chunk-3-1.png
diff --git a/man/figures/README-unnamed-chunk-4-1.png b/man/figures/README-unnamed-chunk-4-1.png
diff --git a/tests/testthat/test-chenAr.R b/tests/testthat/test-chenAr.R
@@ -1,23 +1,18 @@
 # ggseg ----
-context("test-chenAr-adapt_scales")
-test_that("Check that ggseg:::adapt_scales is working", {
-  expect_equal(mode(ggseg:::adapt_scales(unnest(chenAr, ggseg))), "list")
-})
-
 context("test-chenAr-palettes")
 test_that("check new palettes work", {
   expect_equal(length(brain_pal("chenAr", package = "ggsegChen")), 12)
 
   expect_error(brain_pal("chenAr"), "not a valid")
 
-  expect_true(all(names(brain_pal("chenAr", package = "ggsegChen")) %in% chenAr$region))
+  expect_true(all(names(brain_pal("chenAr", package = "ggsegChen")) %in% brain_regions(chenAr)))
 })
 
 context("test-chenAr-ggseg-atlas")
 test_that("atlases are true ggseg atlases", {
 
-  expect_true(is_ggseg_atlas(chenAr))
-
+  expect_true(is_brain_atlas(chenAr))
+  expect_true(is_ggseg_atlas(as_ggseg_atlas(chenAr)))
 })
 
 context("test-chenAr-ggseg")

diff --git a/tests/testthat/test-chenTh.R b/tests/testthat/test-chenTh.R
@@ -1,22 +1,18 @@
 # ggseg ----
-context("test-chenTh-adapt_scales")
-test_that("Check that ggseg:::adapt_scales is working", {
-  expect_equal(mode(ggseg:::adapt_scales(unnest(chenTh, ggseg))), "list")
-})
 
 context("test-chenTh-palettes")
 test_that("check new palettes work", {
   expect_equal(length(brain_pal("chenTh", package = "ggsegChen")), 12)
 
   expect_error(brain_pal("chenTh"), "not a valid")
 
-  expect_true(all(names(brain_pal("chenTh", package = "ggsegChen")) %in% chenTh$region))
+  expect_true(all(names(brain_pal("chenTh", package = "ggsegChen")) %in% brain_regions(chenTh)))
 })
 
 context("test-chenTh-ggseg-atlas")
 test_that("atlases are true ggseg atlases", {
-
-  expect_true(is_ggseg_atlas(chenTh))
+  expect_true(is_brain_atlas(chenTh))
+  expect_true(is_ggseg_atlas(as_ggseg_atlas(chenTh)))
 
 })