From b72c5dd897aca3332a58e143157614f09280be1a Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 1 Nov 2022 11:24:27 -0400 Subject: [PATCH 1/9] bump x.y.z version to even y prior to creation of RELEASE_3_16 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index faba1f3a..0ebd1f17 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: miaViz Title: Microbiome Analysis Plotting and Visualization -Version: 1.5.4 +Version: 1.6.0 Authors@R: c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"), email = "felix.gm.ernst@outlook.com", From 4fa9714ae2d6cdfe6ef5ef9870d2ed0fef58b88a Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 1 Nov 2022 11:24:27 -0400 Subject: [PATCH 2/9] bump x.y.z version to odd y following creation of RELEASE_3_16 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0ebd1f17..cb057cb5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: miaViz Title: Microbiome Analysis Plotting and Visualization -Version: 1.6.0 +Version: 1.7.0 Authors@R: c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"), email = "felix.gm.ernst@outlook.com", From 77c01513f17b1cfb1164f89b21540443da71aa82 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 25 Apr 2023 11:28:01 -0400 Subject: [PATCH 3/9] bump x.y.z version to even y prior to creation of RELEASE_3_17 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8b92f428..37bbb8c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: miaViz Title: Microbiome Analysis Plotting and Visualization -Version: 1.7.5 +Version: 1.8.0 Authors@R: c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", From f8ea3b82a1de5f2775cfd11755633442065fe3d5 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 25 Apr 2023 11:28:01 -0400 Subject: [PATCH 4/9] bump x.y.z version to odd y following creation of RELEASE_3_17 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 37bbb8c4..d4fc1dfc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: miaViz Title: Microbiome Analysis Plotting and Visualization -Version: 1.8.0 +Version: 1.9.0 Authors@R: c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", From 9ade5c3be7cc481f946fbb7012fb59f1b3152c2f Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Mon, 2 Oct 2023 16:04:43 +0300 Subject: [PATCH 5/9] up --- DESCRIPTION | 3 +-- vignettes/miaViz.Rmd | 12 ++++++------ 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f35c3dae..394b43fb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -60,8 +60,7 @@ Suggests: patchwork, vegan, microbiomeDataSets, - bluster, - miaTime + bluster Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 VignetteBuilder: knitr diff --git a/vignettes/miaViz.Rmd b/vignettes/miaViz.Rmd index 99b0dc2c..7a599d46 100644 --- a/vignettes/miaViz.Rmd +++ b/vignettes/miaViz.Rmd @@ -329,7 +329,7 @@ plotDMNFit(dmn_se, type = "laplace") # Serial data ordination and trajectories -```{r, error=FALSE, warning=FALSE, results='hide'} +```{r, eval=FALSE} if(!requireNamespace("devtools", quietly = TRUE)){ BiocManager::install("devtools") } @@ -341,7 +341,7 @@ if(!requireNamespace("miaTime", quietly = TRUE)){ Principal Coordinates Analysis using Bray-Curtis dissimilarity on the `hitchip1006` dataset: -```{r MDS, include=FALSE} +```{r MDS, eval=FALSE} library(miaTime) data(hitchip1006, package = "miaTime") tse <- hitchip1006 @@ -356,7 +356,7 @@ p Retrieving information about all available trajectories: -```{r} +```{r, eval=FALSE} library(dplyr) # List subjects with two time points @@ -369,7 +369,7 @@ table(table(tse$subject)) %>% as.data.frame() %>% Lets look at all trajectories having two time points in the data: -```{r} +```{r, eval=FALSE} # plot p + geom_path(aes(x=X1, y=X2, group=subject), arrow=arrow(length = unit(0.1, "inches")), @@ -383,7 +383,7 @@ p + geom_path(aes(x=X1, y=X2, group=subject), Filtering the two time point trajectories by divergence and displaying top 10%: -```{r} +```{r, eval=FALSE} library(miaTime) # calculating step wise divergence based on the microbial profiles tse <- getStepwiseDivergence(tse, group = "subject", time_field = "time") @@ -411,7 +411,7 @@ p + geom_path(aes(x=X1, y=X2, Plotting an example of the trajectory with the maximum total divergence: -```{r} +```{r, eval=FALSE} # Get subject with the maximum total divergence selected.subject <- data.frame(reducedDim(tse), colData(tse)) %>% group_by(subject) %>% From 50eeb9bb279e86baac93786d8197c01bded9465b Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Mon, 2 Oct 2023 17:31:28 +0300 Subject: [PATCH 6/9] up --- tests/testthat/test-2plotSeries.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-2plotSeries.R b/tests/testthat/test-2plotSeries.R index 817e3a03..b509ae04 100644 --- a/tests/testthat/test-2plotSeries.R +++ b/tests/testthat/test-2plotSeries.R @@ -4,7 +4,7 @@ test_that("plot series", { # Load data from miaTime package if( !require("miaTime") ){ if( !require("devtools") ){ - install.packages("devtools") + BiocManager::install("devtools") } devtools::install_github("microbiome/miaTime") library("miaTime") From c68d5ce03200785493be6b9d55bf32ccd346f5b7 Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Thu, 5 Oct 2023 09:51:27 +0300 Subject: [PATCH 7/9] up --- vignettes/miaViz.Rmd | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/vignettes/miaViz.Rmd b/vignettes/miaViz.Rmd index 7a599d46..864d1252 100644 --- a/vignettes/miaViz.Rmd +++ b/vignettes/miaViz.Rmd @@ -256,7 +256,19 @@ plotColGraph(altExp(GlobalPatterns,"Genus"), # Plotting of serial data -```{r} +```{r, eval=FALSE} +# miaTime is not in Bioc or CRAN. Package needs to be there if it is utilized +# in vignette. That is why miaTime-related chunks are eval=FALSE. Remove these +# when miaTime is in Bioc. +if(!requireNamespace("devtools", quietly = TRUE)){ + BiocManager::install("devtools") +} +if(!requireNamespace("miaTime", quietly = TRUE)){ + devtools::install_github("microbiome/miaTime", upgrade = "never") +} +``` + +```{r, eval=FALSE} # Load data from miaTime package library("miaTime") data(SilvermanAGutData, package="miaTime") @@ -271,7 +283,7 @@ descriptor for ordering the data. The `y` argument selects the feature to show. Since plotting a lot of features is not advised a maximum of 20 features can plotted at the same time. -```{r} +```{r, eval=FALSE} plotSeries(tse, x = "DAY_ORDER", y = taxa, @@ -281,7 +293,7 @@ If replicated data is present, data is automatically used for calculation of the `mean` and `sd` and plotted as a range. Data from different assays can be used for plotting via the `assay.type`. -```{r} +```{r, eval=FALSE} plotSeries(tse[taxa,], x = "DAY_ORDER", colour_by = "Family", @@ -291,7 +303,7 @@ plotSeries(tse[taxa,], Additional variables can be used to modify line type aesthetics. -```{r} +```{r, eval=FALSE} plotSeries(tse, x = "DAY_ORDER", y = getTopTaxa(tse, 5), @@ -329,15 +341,6 @@ plotDMNFit(dmn_se, type = "laplace") # Serial data ordination and trajectories -```{r, eval=FALSE} -if(!requireNamespace("devtools", quietly = TRUE)){ - BiocManager::install("devtools") -} -if(!requireNamespace("miaTime", quietly = TRUE)){ - devtools::install_github("microbiome/miaTime", upgrade = "never") -} -``` - Principal Coordinates Analysis using Bray-Curtis dissimilarity on the `hitchip1006` dataset: From 6cf407243202b3317a4e94f6aa8c8e1d4432f2ff Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Thu, 5 Oct 2023 10:11:42 +0300 Subject: [PATCH 8/9] up --- vignettes/miaViz.Rmd | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/vignettes/miaViz.Rmd b/vignettes/miaViz.Rmd index d4fa5c2a..23debfc6 100644 --- a/vignettes/miaViz.Rmd +++ b/vignettes/miaViz.Rmd @@ -256,18 +256,6 @@ plotColGraph(altExp(GlobalPatterns,"Genus"), # Plotting of serial data -```{r, eval=FALSE} -# miaTime is not in Bioc or CRAN. Package needs to be there if it is utilized -# in vignette. That is why miaTime-related chunks are eval=FALSE. Remove these -# when miaTime is in Bioc. -if(!requireNamespace("devtools", quietly = TRUE)){ - BiocManager::install("devtools") -} -if(!requireNamespace("miaTime", quietly = TRUE)){ - devtools::install_github("microbiome/miaTime", upgrade = "never") -} -``` - ```{r, eval=FALSE} # Load data from miaTime package library("miaTime") From d40893bc002fbdf1061008761d4ff1e3272239bf Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Thu, 5 Oct 2023 10:42:19 +0300 Subject: [PATCH 9/9] up --- vignettes/miaViz.Rmd | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/vignettes/miaViz.Rmd b/vignettes/miaViz.Rmd index 23debfc6..ef2b41b9 100644 --- a/vignettes/miaViz.Rmd +++ b/vignettes/miaViz.Rmd @@ -256,6 +256,15 @@ plotColGraph(altExp(GlobalPatterns,"Genus"), # Plotting of serial data +```{r, eval=FALSE} +if(!requireNamespace("devtools", quietly = TRUE)){ + BiocManager::install("devtools") +} +if(!requireNamespace("miaTime", quietly = TRUE)){ + devtools::install_github("microbiome/miaTime", upgrade = "never") +} +``` + ```{r, eval=FALSE} # Load data from miaTime package library("miaTime") @@ -329,15 +338,6 @@ plotDMNFit(dmn_se, type = "laplace") # Serial data ordination and trajectories -```{r, eval=FALSE} -if(!requireNamespace("devtools", quietly = TRUE)){ - BiocManager::install("devtools") -} -if(!requireNamespace("miaTime", quietly = TRUE)){ - devtools::install_github("microbiome/miaTime", upgrade = "never") -} -``` - Principal Coordinates Analysis using Bray-Curtis dissimilarity on the `hitchip1006` dataset: