Skip to content

Commit

Permalink
Merge branch 'devel' into devel
Browse files Browse the repository at this point in the history
  • Loading branch information
antagomir authored May 21, 2024
2 parents 3375c9c + 9ed45eb commit e1b3df5
Show file tree
Hide file tree
Showing 11 changed files with 161 additions and 340 deletions.
276 changes: 0 additions & 276 deletions .github/workflows/check-bioc-devel.yml

This file was deleted.

57 changes: 57 additions & 0 deletions .github/workflows/rworkflows.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
name: rworkflows
'on':
push:
branches:
- master
- main
- devel
- RELEASE_**
pull_request:
branches:
- master
- main
- devel
- RELEASE_**
jobs:
rworkflows:
permissions: write-all
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
strategy:
fail-fast: ${{ false }}
matrix:
config:
- os: ubuntu-latest
bioc: devel
r: auto
cont: ghcr.io/bioconductor/bioconductor_docker:devel
rspm: ~
- os: macOS-latest
bioc: devel
r: auto
cont: ~
rspm: ~
- os: windows-latest
bioc: devel
r: auto
cont: ~
rspm: ~
steps:
- uses: neurogenomics/rworkflows@master
with:
run_bioccheck: ${{ false }}
run_rcmdcheck: ${{ true }}
as_cran: ${{ true }}
run_vignettes: ${{ true }}
has_testthat: ${{ true }}
run_covr: ${{ true }}
run_pkgdown: ${{ true }}
has_runit: ${{ false }}
has_latex: ${{ false }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run_docker: ${{ false }}
DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
runner_os: ${{ runner.os }}
cache_version: cache-v1
docker_registry: ghcr.io
4 changes: 3 additions & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: miaViz
Title: Microbiome Analysis Plotting and Visualization
Version: 1.11.2
Version: 1.13.1
Authors@R:
c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
email = "[email protected]",
Expand Down Expand Up @@ -61,6 +61,8 @@ Suggests:
vegan,
microbiomeDataSets,
bluster
Remotes:
github::microbiome/miaTime
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr
1 change: 1 addition & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(ape,as.phylo)
importFrom(ape,drop.tip)
importFrom(ape,keep.tip)
importFrom(ape,rotateConstr)
importFrom(dplyr,"%>%")
Expand Down
3 changes: 3 additions & 0 deletions NEWS
Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,6 @@ Changes in version 1.9.x

Changes in version 1.11.x
+ replace addTaxonomyTree with addHierarchyTree after renaming in mia package

Changes in version 1.13.x
+ plot*Tree: bugfix, ununique nodes
6 changes: 3 additions & 3 deletions R/plotCCA.R
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@
#' @param label.color Alias for `label.colour`.
#'
#' @param sep.group String specifying the separator used in the labels.
#' (default: \code{sep.group = "\U2012"})
#' (default: \code{sep.group = "\U2014"})
#'
#' @param repl.underscore String used to replace underscores in the labels.
#' (default: \code{repl.underscore = " "})
Expand Down Expand Up @@ -182,7 +182,7 @@ setMethod("plotRDA", signature = c(object = "SingleCellExperiment"),
add.ellipse = TRUE, ellipse.alpha = 0.2, ellipse.linewidth = 0.1, ellipse.linetype = 1,
vec.size = 0.5, vec.color = vec.colour, vec.colour = "black", vec.linetype = 1,
arrow.size = 0.25, label.color = label.colour, label.colour = "black", label.size = 4,
vec.text = TRUE, repel.labels = TRUE, sep.group = "\U2012", repl.underscore = " ",
vec.text = TRUE, repel.labels = TRUE, sep.group = "\U2014", repl.underscore = " ",
add.significance = TRUE, add.expl.var = TRUE, add.vectors = TRUE, parse.labels = TRUE, ...){
###################### Input check ########################
if( !(add.ellipse %in% c(TRUE, FALSE, "fill", "color", "colour")) ){
Expand Down Expand Up @@ -441,7 +441,7 @@ setMethod("plotRDA", signature = c(object = "matrix"),
# Make vector labels more tidy, i.e, separate variable and group names.
# Replace also underscores with space
.tidy_vector_labels <- function(
vector_label, coldata, sep.group = "\U2012", repl.underscore = " ", ...){
vector_label, coldata, sep.group = "\U2014", repl.underscore = " ", ...){
# Get variable names from sample metadata
var_names <- colnames(coldata)
# Loop through vector labels
Expand Down
Loading

0 comments on commit e1b3df5

Please sign in to comment.