From b8b345ad57bdb2178097bd6aee568d910d7dca90 Mon Sep 17 00:00:00 2001 From: Sam Hillman Date: Tue, 4 Jun 2024 14:14:42 +0300 Subject: [PATCH 1/2] updated example in docs --- R/plotAbundance.R | 4 ++-- man/plotAbundance.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/plotAbundance.R b/R/plotAbundance.R index 29f2adad..b6df4844 100644 --- a/R/plotAbundance.R +++ b/R/plotAbundance.R @@ -72,8 +72,8 @@ #' data(GlobalPatterns, package="mia") #' se <- GlobalPatterns #' -#' ## Plotting abundance using the first taxonomic rank as default -#' plotAbundance(se, assay.type="counts") +#' ## Plotting counts using the first taxonomic rank as default +#' plotAbundance(se, assay.type="counts", use_relative=FALSE) + labs(y="Counts") #' #' ## Using "Phylum" as rank #' plotAbundance(se, assay.type="counts", rank = "Phylum", add_legend = FALSE) diff --git a/man/plotAbundance.Rd b/man/plotAbundance.Rd index eb29a844..5a234fd6 100644 --- a/man/plotAbundance.Rd +++ b/man/plotAbundance.Rd @@ -96,8 +96,8 @@ features present. data(GlobalPatterns, package="mia") se <- GlobalPatterns -## Plotting abundance using the first taxonomic rank as default -plotAbundance(se, assay.type="counts") +## Plotting counts using the first taxonomic rank as default +plotAbundance(se, assay.type="counts", use_relative=FALSE) + labs(y="Counts") ## Using "Phylum" as rank plotAbundance(se, assay.type="counts", rank = "Phylum", add_legend = FALSE) From a5c80257d0fad5417dc5a00aa6731b1784ab4680 Mon Sep 17 00:00:00 2001 From: Sam Hillman Date: Thu, 6 Jun 2024 15:42:00 +0300 Subject: [PATCH 2/2] ran all contibutor checks - no errors relating to my PR, and fixed typo in a unittest, edited gitignore/Rbuildignore --- .Rbuildignore | 3 +++ .gitignore | 3 +++ tests/testthat/test-2plotSeries.R | 2 +- 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 0f56b95e..c1bd9a89 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ +^renv$ +^renv\.lock$ ^miaViz\.Rproj$ ^\.Rproj\.user$ .github @@ -7,3 +9,4 @@ inst/extras/ ^doc$ ^Meta$ +^\.Rprofile$ diff --git a/.gitignore b/.gitignore index 2bab5502..fa29b55a 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,6 @@ docs .DS_Store /doc/ /Meta/ +renv/ +.Rprofile + diff --git a/tests/testthat/test-2plotSeries.R b/tests/testthat/test-2plotSeries.R index 7970a643..6ba2ee90 100644 --- a/tests/testthat/test-2plotSeries.R +++ b/tests/testthat/test-2plotSeries.R @@ -2,7 +2,7 @@ context("plot series") test_that("plot series", { # Load data from miaTime package - skip_if_not_installed("miatime") + skip_if_not_installed("miaTime") data(SilvermanAGutData, package = "miaTime") tse <- SilvermanAGutData tse_sub <- tse[1:5]