Fix IMPORTS (#41)

* up * up
EBI-Metagenomics · Mar 28, 2024 · 62eae97 · 62eae97
1 parent 60c01d2
commit 62eae97
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MGnifyR
 Type: Package
-Version: 0.99.27
+Version: 0.99.28
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -21,25 +21,24 @@ License: Artistic-2.0 | file LICENSE
 Encoding: UTF-8
 Depends:
     R(>= 4.4.0),
-    mia,
     MultiAssayExperiment,
     TreeSummarizedExperiment,
     SummarizedExperiment,
-    biomformat,
     BiocGenerics
 Imports:
+    mia,
     ape,
     dplyr,
     httr,
     methods,
     plyr,
     reshape2,
     S4Vectors,
-    stats,
     urltools,
     utils,
     tidyjson
 Suggests:
+    biomformat,
     broom,
     ggplot2,
     knitr,

diff --git a/vignettes/MGnifyR.Rmd b/vignettes/MGnifyR.Rmd
@@ -175,6 +175,8 @@ microbiome data manipulation and visualization. Moreover, it enables access
 to `miaverse` tools. For example, we can estimate diversity of samples...
 
 ```{r calculate_diversity, fig.width=9}
+library(mia)
+
 mae[[1]] <- estimateDiversity(mae[[1]], index = "shannon")
 
 library(scater)

diff --git a/vignettes/MGnifyR_long.Rmd b/vignettes/MGnifyR_long.Rmd
@@ -256,6 +256,8 @@ microbiome data manipulation and visualization. Moreover, it enables access
 to `miaverse` tools. For example, we can estimate diversity of samples.
 
 ```{r calculate_diversity}
+library(mia)
+
 tse <- estimateDiversity(tse, index = "shannon")
 
 library(scater)