From e62391e1705ba5fde3eebc7b8fa3d4142298e655 Mon Sep 17 00:00:00 2001 From: artur-sannikov Date: Wed, 1 Oct 2025 05:44:08 +0000 Subject: [PATCH 01/49] Update oma_packages.csv --- oma_packages/oma_packages.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/oma_packages/oma_packages.csv b/oma_packages/oma_packages.csv index c1306867..3adc3c0d 100644 --- a/oma_packages/oma_packages.csv +++ b/oma_packages/oma_packages.csv @@ -5,6 +5,7 @@ biclust BiocBook BiocManager BiocParallel +BiocStyle Biostrings bluster caret From ed4a7f42f4768951634210ada11903400928cbf8 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 10:52:32 +0200 Subject: [PATCH 02/49] chore: substitute analyse and summarise --- inst/pages/extra_material/add-comm-typing.Rmd | 6 +++--- inst/pages/machine_learning.qmd | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index 5986173d..42791a96 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -134,7 +134,7 @@ res <- lapply(k, ClustDiagPlot) ### Composition barplot -A typical way to visualise microbiome composition is by using a composition barplot. +A typical way to visualize microbiome composition is by using a composition barplot. In the following, we agglomerate to the phylum level and subset by the country "Finland" to avoid long computation times. The samples in the barplot are ordered by "Firmicutes": ```{r, message=FALSE, warning=FALSE} @@ -155,7 +155,7 @@ plotAbundance(tse, rank = "Phylum", order.row.by = "abund", order.col.by = "Firm ### Composition heatmap -The community composition can be visualised with a heatmap where one axis represents the samples and the other taxa. The colour of each line represents the abundance of a taxon in a specific sample. +The community composition can be visualized with a heatmap where one axis represents the samples and the other taxa. The colour of each line represents the abundance of a taxon in a specific sample. Here, the CLR + Z-transformed abundances are shown. @@ -282,7 +282,7 @@ factoextra::fviz_nbclust(x, kmeans, method = "gap_stat", nboot = 50)+ The peak suggests $k=6$ clusters. If we also look to the points where the graph jumps, we can see there is evidence for $k=2$, $k=6$, and $k=8$. The output indicates that there should be at least three clusters present. Since we have previous evidence for the existence of six clusters from the silhouette and elbow methods, we will go with $k=6$. -At this point it helps to visualise the clustering in an MDS or NMDS plot. +At this point it helps to visualize the clustering in an MDS or NMDS plot. Now, let's divide the subjects into their respective clusters. diff --git a/inst/pages/machine_learning.qmd b/inst/pages/machine_learning.qmd index ad857eb7..b400d6cc 100644 --- a/inst/pages/machine_learning.qmd +++ b/inst/pages/machine_learning.qmd @@ -125,7 +125,7 @@ table(tse[["disease"]]) |> Before applying any ML algorithm, the data must be preprocessed. This speeds up the training of the models by reducing the amount of -features analysed, a desirable outcome when working with +features analyzed, a desirable outcome when working with high-dimensional microbiome data. In addition to faster performance, common pre-processing steps have biological justifications. For instance: @@ -679,7 +679,7 @@ roc_p + prc_p + plot_layout(guides = "collect") Before describing the plots and their meaning, it is worth noting that the ROC curves of both models resembles the curve presented in -the article where this dataset was first analysed [@qin2012_t2d] +the article where this dataset was first analyzed [@qin2012_t2d] (see Figure 4B). Interestingly, authors used other supervised ML algorithm, and it was trained in a set of 50 microbiome genes (instead of taxonomic features and alpha diversity metrics, as we did). However, it is From f3fc6390def4665691911fd5340ea42369dc6d26 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 10:56:30 +0200 Subject: [PATCH 03/49] substitute analyse --- inst/pages/correlation.qmd | 2 +- inst/pages/machine_learning.qmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/correlation.qmd b/inst/pages/correlation.qmd index 9601c45e..7773e9dc 100644 --- a/inst/pages/correlation.qmd +++ b/inst/pages/correlation.qmd @@ -19,7 +19,7 @@ we will demonstrate how to perform correlation analysis with ## Association between taxonomic features -Here we demonstrate how to analyse which bacteria co-exists in the dataset. +Here we demonstrate how to analyze which bacteria co-exists in the dataset. ```{r} #| label: association1 diff --git a/inst/pages/machine_learning.qmd b/inst/pages/machine_learning.qmd index b400d6cc..09261cef 100644 --- a/inst/pages/machine_learning.qmd +++ b/inst/pages/machine_learning.qmd @@ -133,7 +133,7 @@ For instance: * **Collapse highly correlated features:** In a microbial community, it's common for the abundance of two or more taxonomic features to be highly correlated. Thus, removing or collapsing correlated features allows the -model to analyse them as one group. +model to analyze them as one group. * **Remove features with near-zero variance:** Features that don't vary enough across groups can hardly help in discerning between them, as they don't hold any biologically relevant information. Additionally, From 7ecb9c32a7e9a6fb2904aba435f0026dac340262 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 10:58:07 +0200 Subject: [PATCH 04/49] substitute favour --- inst/pages/alpha_diversity.qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/alpha_diversity.qmd b/inst/pages/alpha_diversity.qmd index 17873f90..08045241 100644 --- a/inst/pages/alpha_diversity.qmd +++ b/inst/pages/alpha_diversity.qmd @@ -34,8 +34,8 @@ evident from their names. @bastiaanssen2023bugs1 lay out this relationship across two factors (See table below); First, alpha diversity metrics can be defined as special cases of a unifying equation of **diversity**, where the **Hill number** determines the specific index captured. Lower Hill numbers -favour **richness**, the number of distinct taxonomic features, whereas higher -numbers favour **evenness**, how the taxonomic features are distributed over +favor **richness**, the number of distinct taxonomic features, whereas higher +numbers favor **evenness**, how the taxonomic features are distributed over the sample [@Hill1973]. Second, some alpha diversity metrics are weighted based on phylogeny, like Faith's PD [-@Faith1992] and PhILR [@Silverman2017]. From b73f0bd7716a7c5e2d47f756735a1a305d37ba89 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 10:59:06 +0200 Subject: [PATCH 05/49] substitute visualisation --- inst/pages/miaverse.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/miaverse.qmd b/inst/pages/miaverse.qmd index 9b80b5dd..b1ba9a5f 100644 --- a/inst/pages/miaverse.qmd +++ b/inst/pages/miaverse.qmd @@ -143,7 +143,7 @@ analysis - `r BiocStyle::Githubpkg("himelmallick/IntegratedLearner")` for multiomics classification and prediction - `r BiocStyle::Biocpkg("iSEEtree")` [@Benedetti2025iseetree] for interactive -visualisation of hierarchical data +visualization of hierarchical data - `r BiocStyle::Biocpkg("lefser")` [@Asya2024] for metagenomic biomarker discovery - `r BiocStyle::Biocpkg("LimROTS")` for differential expression analysis for From 90d80f2749559765c1a696628db7b46a0b23bd96 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:02:42 +0200 Subject: [PATCH 06/49] subsitute colour --- inst/pages/alpha_diversity.qmd | 2 +- inst/pages/community_similarity.qmd | 4 ++-- inst/pages/extra_material/visualization.qmd | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/inst/pages/alpha_diversity.qmd b/inst/pages/alpha_diversity.qmd index 08045241..d95ae79c 100644 --- a/inst/pages/alpha_diversity.qmd +++ b/inst/pages/alpha_diversity.qmd @@ -182,7 +182,7 @@ barcode). ```{r} #| label: plot_richness #| message: false -#| fig-cap: "Observed richness plotted grouped by sample type with colour-labelled barcode." +#| fig-cap: "Observed richness plotted grouped by sample type with color-labelled barcode." library(scater) plotColData( diff --git a/inst/pages/community_similarity.qmd b/inst/pages/community_similarity.qmd index a237d5e5..dfe597e3 100644 --- a/inst/pages/community_similarity.qmd +++ b/inst/pages/community_similarity.qmd @@ -786,7 +786,7 @@ the `plotRDA()` function from the `r BiocStyle::Biocpkg("miaViz")` package. # Load packages for plotting function library(miaViz) -# Generate RDA plot coloured by clinical status +# Generate RDA plot colored by clinical status plotRDA(tse2, "RDA", colour.by = "ClinicalStatus") ``` @@ -1101,7 +1101,7 @@ eigenvalues? 6. Visualize the first two principal components. 7. Explore `colData` and visualize the first two principal components again, -now with samples coloured based on a variable from the sample metadata. Can you +now with samples colored based on a variable from the sample metadata. Can you observe any patterns? 8. Visualize the PCA loadings for the two first components. Which features have diff --git a/inst/pages/extra_material/visualization.qmd b/inst/pages/extra_material/visualization.qmd index a14355ae..d58ae5a3 100644 --- a/inst/pages/extra_material/visualization.qmd +++ b/inst/pages/extra_material/visualization.qmd @@ -222,7 +222,7 @@ which is explained in chapter [@sec-extras]. # perform NMDS coordination method tse <- runNMDS(tse, FUN = vegan::vegdist, name = "NMDS") # plot results of a 2-component NMDS on tse, -# coloured-scaled by shannon diversity index +# colored-scaled by shannon diversity index plotReducedDim(tse, "NMDS", colour_by = "shannon") ``` @@ -241,7 +241,7 @@ tse <- addMDS( ncomponents = 3 ) # plot results of a 3-component MDS on tse, -# coloured-scaled by faith diversity index +# colored-scaled by faith diversity index plotReducedDim(tse, "MDS", ncomponents = c(1:3), colour_by = "faith") ``` From 2f9e8a9a6378f1fb1358be68112cdccb776895a5 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:04:23 +0200 Subject: [PATCH 07/49] substitute utilise --- inst/pages/extra_material/add-comm-typing.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index 42791a96..ea4a4848 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -196,7 +196,7 @@ grid.text("Phylum", x = -0.04, y = 0.47, rot = 90, gp = gpar(fontsize = 16)) ## Cluster into CSTs -The burden of specifying the number of clusters falls on the researcher. To help make an informed decision, we turn to previously established methods for doing so. In this section we introduce three such methods (aside from DMM analysis) to cluster similar samples. They include the [Elbow Method, Silhouette Method, and Gap Statistic Method](https://uc-r.github.io/kmeans_clustering). All of them will utilise the [`kmeans'](https://uc-r.github.io/kmeans_clustering) algorithm which essentially assigns clusters and minimises the distance within clusters (a sum of squares calculation). The default distance metric used is the Euclidean metric. +The burden of specifying the number of clusters falls on the researcher. To help make an informed decision, we turn to previously established methods for doing so. In this section we introduce three such methods (aside from DMM analysis) to cluster similar samples. They include the [Elbow Method, Silhouette Method, and Gap Statistic Method](https://uc-r.github.io/kmeans_clustering). All of them will utilize the [`kmeans'](https://uc-r.github.io/kmeans_clustering) algorithm which essentially assigns clusters and minimises the distance within clusters (a sum of squares calculation). The default distance metric used is the Euclidean metric. The scree plot allows us to see how much of the variance is captured by each dimension in the MDS ordination. From 7aa956f92f145b31b6cbc101240331221892e1d5 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:05:42 +0200 Subject: [PATCH 08/49] substitute maximize --- inst/pages/extra_material/add-comm-typing.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index ea4a4848..288daee7 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -260,7 +260,7 @@ The function says that the bend occurs at $k=3$, however it is hard to tell that ### Silhouette Method -This method on the otherhand returns a width for each $k$. In this case, we want the $k$ that maximises the width. +This method on the otherhand returns a width for each $k$. In this case, we want the $k$ that maximizes the width. ```{r silhouette} # Silhouette method @@ -272,7 +272,7 @@ The graph shows the maximum occurring at $k=6$. At the very least, there is stro ### Gap-Statistic Method -The Gap-Statistic Method is the most complicated among the methods discussed here. With the gap statistic method, we typically want the $k$ value that maximises the output (local and global maxima), but we also want to pay attention to where the plot jumps if the maximum value doesn't turn out to be helpful. +The Gap-Statistic Method is the most complicated among the methods discussed here. With the gap statistic method, we typically want the $k$ value that maximizes the output (local and global maxima), but we also want to pay attention to where the plot jumps if the maximum value doesn't turn out to be helpful. ```{r gap-statistic} # Gap Statistic Method From 9c25d60e298309e0bbce9d0f2bbee977bd11bde4 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:10:43 +0200 Subject: [PATCH 09/49] substitute programme --- inst/pages/contributions.qmd | 2 +- inst/pages/support.qmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/contributions.qmd b/inst/pages/contributions.qmd index 9e378d7d..d403e481 100644 --- a/inst/pages/contributions.qmd +++ b/inst/pages/contributions.qmd @@ -249,7 +249,7 @@ This work has been supported by: * [Research Council of Finland](https://www.aka.fi/) * [FindingPheno](https://www.findingpheno.eu/) European Union’s Horizon 2020 -research and innovation programme under grant agreement No 952914 +research and innovation program under grant agreement No 952914 * COST Action network on Statistical and Machine Learning Techniques for Human Microbiome Studies diff --git a/inst/pages/support.qmd b/inst/pages/support.qmd index 2a4cc537..2f57e39b 100644 --- a/inst/pages/support.qmd +++ b/inst/pages/support.qmd @@ -2,7 +2,7 @@ ## FindingPheno -This project received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 952914 ([FindingPheno](https://findingpheno.eu/)). +This project received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 952914 ([FindingPheno](https://findingpheno.eu/)). ## Online support From 9933f4d69ec270f2a81cc1903184ed3f3fc26c2c Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:14:08 +0200 Subject: [PATCH 10/49] substitute normalis --- inst/pages/transformation.qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/transformation.qmd b/inst/pages/transformation.qmd index 28c7167d..19db2d7b 100644 --- a/inst/pages/transformation.qmd +++ b/inst/pages/transformation.qmd @@ -15,7 +15,7 @@ interpretable values, to enhance the comparability of samples/features or to make data compatible with the assumptions of certain statistical methods. Examples include transforming feature counts into relative abundances -(i.e., "normalising as proportions"), or with compositionality-aware +(i.e., "normalizing as proportions"), or with compositionality-aware transformations such as the centered log-ratio transformation (clr). ## Characteristics of microbiome data to inform data transformations {#sec-stat-challenges} @@ -99,7 +99,7 @@ ranks. This has use, for instance, in non-parametric statistics. allows data with zeroes and avoids the need to add pseudocount [@Keshavan2010; @Martino2019]. -- **relabundance**: Relative transformation, also known as normalising as +- **relabundance**: Relative transformation, also known as normalizing as proportions, total sum scaling (TSS) and compositional transformation. This converts counts into proportions (at the scale [0, 1]) that sum up to 1. Much of the currently available taxonomic abundance data from From d621ed0259dce0d479a50c52f9766375d990f5a4 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:17:57 +0200 Subject: [PATCH 11/49] substitute artefact --- inst/pages/subsetting.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/subsetting.qmd b/inst/pages/subsetting.qmd index 0040af22..c790b774 100644 --- a/inst/pages/subsetting.qmd +++ b/inst/pages/subsetting.qmd @@ -285,7 +285,7 @@ we opted for a rather conservative threshold that retains most features. We can subset the data based on prevalence using `subsetByPrevalent()`, which filters features that exceed a specified prevalence threshold, -helping to remove rare features that may be artefacts. Conversely, +helping to remove rare features that may be artifacts. Conversely, `subsetByRare()` allows us to retain only features below the threshold, enabling a focus on rare features within the dataset. From 83f0376e27e2fa9a76b8d70620866867f1880c53 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:20:28 +0200 Subject: [PATCH 12/49] substitute label --- inst/pages/alpha_diversity.qmd | 2 +- inst/pages/clustering.qmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/alpha_diversity.qmd b/inst/pages/alpha_diversity.qmd index d95ae79c..dcc120ec 100644 --- a/inst/pages/alpha_diversity.qmd +++ b/inst/pages/alpha_diversity.qmd @@ -182,7 +182,7 @@ barcode). ```{r} #| label: plot_richness #| message: false -#| fig-cap: "Observed richness plotted grouped by sample type with color-labelled barcode." +#| fig-cap: "Observed richness plotted grouped by sample type with color-labeled barcode." library(scater) plotColData( diff --git a/inst/pages/clustering.qmd b/inst/pages/clustering.qmd index 32096105..514a7ea4 100644 --- a/inst/pages/clustering.qmd +++ b/inst/pages/clustering.qmd @@ -118,7 +118,7 @@ clusters to describe the data. Now, we visualize the hierarchical structure of the clusters with a dendrogram tree. In dendrograms, the tree is split where the branch length is the largest. In each splitting point, the tree is divided into two clusters leading to the -hierarchy. In this example, each sample is labelled by their dominant taxon +hierarchy. In this example, each sample is labeled by their dominant taxon to visualize ecological differences between the clusters. ```{r} From 91d3249c67d621ceec985bbe4420272204a3b4d6 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:22:06 +0200 Subject: [PATCH 13/49] substitute minimis --- inst/pages/extra_material/add-comm-typing.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index 288daee7..d6867fdd 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -196,7 +196,7 @@ grid.text("Phylum", x = -0.04, y = 0.47, rot = 90, gp = gpar(fontsize = 16)) ## Cluster into CSTs -The burden of specifying the number of clusters falls on the researcher. To help make an informed decision, we turn to previously established methods for doing so. In this section we introduce three such methods (aside from DMM analysis) to cluster similar samples. They include the [Elbow Method, Silhouette Method, and Gap Statistic Method](https://uc-r.github.io/kmeans_clustering). All of them will utilize the [`kmeans'](https://uc-r.github.io/kmeans_clustering) algorithm which essentially assigns clusters and minimises the distance within clusters (a sum of squares calculation). The default distance metric used is the Euclidean metric. +The burden of specifying the number of clusters falls on the researcher. To help make an informed decision, we turn to previously established methods for doing so. In this section we introduce three such methods (aside from DMM analysis) to cluster similar samples. They include the [Elbow Method, Silhouette Method, and Gap Statistic Method](https://uc-r.github.io/kmeans_clustering). All of them will utilize the [`kmeans'](https://uc-r.github.io/kmeans_clustering) algorithm which essentially assigns clusters and minimizes the distance within clusters (a sum of squares calculation). The default distance metric used is the Euclidean metric. The scree plot allows us to see how much of the variance is captured by each dimension in the MDS ordination. From f0a3c8c4b4a75dddc1bd5dda41a63d0809d00086 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:24:11 +0200 Subject: [PATCH 14/49] substitute grey --- inst/pages/machine_learning.qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/machine_learning.qmd b/inst/pages/machine_learning.qmd index 09261cef..3f339953 100644 --- a/inst/pages/machine_learning.qmd +++ b/inst/pages/machine_learning.qmd @@ -686,7 +686,7 @@ of taxonomic features and alpha diversity metrics, as we did). However, it is interesting that concordant AUCs and ROC curves shapes were obtained using different microbiome-derived information. -Regarding our figures, note the dashed grey lines in both plots +Regarding our figures, note the dashed gray lines in both plots representing the expected performance of a model that is classifying samples randomly. Therefore, the greater the distance between that reference and the line representing our model's performance, the better. @@ -774,7 +774,7 @@ obs_vs_pred <- obs_vs_pred + labs(x = "Predicted BMI", y = "Observed BMI") obs_vs_pred + theme_bw() ``` -The dashed grey line in the plot above represents a perfect correlation +The dashed gray line in the plot above represents a perfect correlation between the observed and the model-predicted BMI values of each participant. Thus, the line indicates perfect performance of the model. We can see that while the predictions are around the mean BMI (close From cbcbded4a6a00bd23dc8133e361cee594f85c119 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:26:48 +0200 Subject: [PATCH 15/49] substitute behaviour --- inst/pages/extra_material/extra_material.qmd | 2 +- inst/pages/mediation.qmd | 2 +- inst/pages/phyloseq_cheatsheet.qmd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/inst/pages/extra_material/extra_material.qmd b/inst/pages/extra_material/extra_material.qmd index a5dbd76f..a88f94e2 100644 --- a/inst/pages/extra_material/extra_material.qmd +++ b/inst/pages/extra_material/extra_material.qmd @@ -407,7 +407,7 @@ under `altExp`. `tax_glom()` removes the taxa which have not been assigned to the level given in taxrank by default (NArm = TRUE). So we will add the na.rm = TRUE to `agglomerateByRank()` function which is -equivalent to the default behaviour of `tax_glom()`. +equivalent to the default behavior of `tax_glom()`. ```{r} #| label: agglomerateByRank diff --git a/inst/pages/mediation.qmd b/inst/pages/mediation.qmd index 26e5fd16..0fcbdf21 100644 --- a/inst/pages/mediation.qmd +++ b/inst/pages/mediation.qmd @@ -29,7 +29,7 @@ $$ The microbiome can mediate the effects of multiple environmental stimuli on human health. However, the importance of its role as a mediator depends on the nature of the stimulus. For example, the effect of dietary fiber intake on host -behaviour is largely mediated by the gut microbiome [@Logan2014nutritional]. In +behavior is largely mediated by the gut microbiome [@Logan2014nutritional]. In contrast, the indirect impact of antibiotic use on mental health through an altered microbiome represents a more subtle process [@Dinan2022antibiotics]. diff --git a/inst/pages/phyloseq_cheatsheet.qmd b/inst/pages/phyloseq_cheatsheet.qmd index 4ddfd4d2..51e647b6 100644 --- a/inst/pages/phyloseq_cheatsheet.qmd +++ b/inst/pages/phyloseq_cheatsheet.qmd @@ -418,7 +418,7 @@ object under `altExp`. `tax_glom()` removes the taxa which have not been assigned to the level given in taxrank by default (NArm = TRUE). So we will add the na.rm = TRUE to -`agglomerateByRank()` function which is equivalent to the default behaviour +`agglomerateByRank()` function which is equivalent to the default behavior of `tax_glom()`. ```{r} From 81520f31dbd512722e1c322634de1ed1e29512c3 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:33:00 +0200 Subject: [PATCH 16/49] substitute whilst --- inst/pages/extra_material/extra_material.qmd | 2 +- inst/pages/phyloseq_cheatsheet.qmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/extra_material/extra_material.qmd b/inst/pages/extra_material/extra_material.qmd index a88f94e2..4229a3a3 100644 --- a/inst/pages/extra_material/extra_material.qmd +++ b/inst/pages/extra_material/extra_material.qmd @@ -189,7 +189,7 @@ Here we'll show an example of how to add relative abundances and CLR normalized OTU tables to your tse assays. With phyloseq you would need three different phyloseq objects, each taking up -7.7 MB of memory, whilst the tse with the three assays takes up only 18.3 MB. +7.7 MB of memory, while the tse with the three assays takes up only 18.3 MB. ```{r} #| label: transform_assay diff --git a/inst/pages/phyloseq_cheatsheet.qmd b/inst/pages/phyloseq_cheatsheet.qmd index 51e647b6..94fef877 100644 --- a/inst/pages/phyloseq_cheatsheet.qmd +++ b/inst/pages/phyloseq_cheatsheet.qmd @@ -194,7 +194,7 @@ OTU tables to your `tse` assays. With `r BiocStyle::Biocpkg("phyloseq")` you would need three different `r BiocStyle::Biocpkg("phyloseq")` objects, each taking up 7.7 MB of memory, -whilst the tse with the three assays takes up only 18.3 MB. +while the tse with the three assays takes up only 18.3 MB. ```{r} #| label: transform_assay From 7aafb9559943d661758781374d4d62a366cf3e14 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 11:36:58 +0200 Subject: [PATCH 17/49] substitute additional colour --- inst/pages/extra_material/add-comm-typing.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index d6867fdd..86ece7b6 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -155,7 +155,7 @@ plotAbundance(tse, rank = "Phylum", order.row.by = "abund", order.col.by = "Firm ### Composition heatmap -The community composition can be visualized with a heatmap where one axis represents the samples and the other taxa. The colour of each line represents the abundance of a taxon in a specific sample. +The community composition can be visualized with a heatmap where one axis represents the samples and the other taxa. The color of each line represents the abundance of a taxon in a specific sample. Here, the CLR + Z-transformed abundances are shown. @@ -307,7 +307,7 @@ library(scater) library(RColorBrewer) library(patchwork) -# set up colours +# set up colors CSTColors <- brewer.pal(6, "Paired")[c(2, 5, 3, 4, 1, 6)] names(CSTColors) <- CSTs From 10b039dc964e9af53438ef2640a50986f047d119 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 15 Jan 2026 16:27:29 +0200 Subject: [PATCH 18/49] substitute summarize --- inst/pages/containers.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/containers.qmd b/inst/pages/containers.qmd index 9871ea3c..4f636d85 100644 --- a/inst/pages/containers.qmd +++ b/inst/pages/containers.qmd @@ -188,7 +188,7 @@ assay(tse, "counts") |> head() In summary, in the world of microbiome analysis, an assay is essentially a way to describe the composition of microbes in a given -sample. This way we can summarise the microbiome profile of a human gut +sample. This way we can summarize the microbiome profile of a human gut or a sample of soil. Furthermore, to illustrate the use of multiple assays, we can create an From 51187d3ee7ef6af2520b9c210205177abc802643 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:15:31 +0200 Subject: [PATCH 19/49] chore: first test of conversion script --- .github/workflows/american-english.yaml | 32 +++++++++++++++++++ .../workflows/convert-british-to-american.sh | 13 ++++++++ convert-british-to-american.sh | 12 +++++++ 3 files changed, 57 insertions(+) create mode 100644 .github/workflows/american-english.yaml create mode 100644 .github/workflows/convert-british-to-american.sh create mode 100755 convert-british-to-american.sh diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml new file mode 100644 index 00000000..53b97034 --- /dev/null +++ b/.github/workflows/american-english.yaml @@ -0,0 +1,32 @@ +on: + pull_request: + branches: + - devel + - RELEASE_** + paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown"] + workflow_dispatch: +name: Convert British English spelling into American English spelling +permissions: read-all +jobs: + convert: + runs-on: ubuntu-latest + permissions: + contents: write + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - name: Checkout repo + uses: actions/checkout@v6 + - name: Convert from American English to British English + run: bash .github/workflows/convert-british-to-american.sh + - name: Commit and push changes + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git add -u + if git diff --cached --quiet; then + echo "No changes to commit." + else + git commit -m "Convert from British to American English" + git push origin HEAD:${{ github.head_ref }} + fi diff --git a/.github/workflows/convert-british-to-american.sh b/.github/workflows/convert-british-to-american.sh new file mode 100644 index 00000000..bd60ef58 --- /dev/null +++ b/.github/workflows/convert-british-to-american.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +set -e + +find . -type f -print0 -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | + xargs -0 sed -i \ + -e 's/visualize/visualize/' \ + -e 's/summarize/summarize/' \ + -e 's/analyzed/analyzed/' \ + -e 's/\/analyze/' \ + -e 's/favor/favor/' \ + -e 's/visualisation/visualization/' \ + -e 's/visualisation/visualization/' diff --git a/convert-british-to-american.sh b/convert-british-to-american.sh new file mode 100755 index 00000000..7ff52b6d --- /dev/null +++ b/convert-british-to-american.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +set -e + +find . -type f -print0 -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | + xargs -0 sed -i \ + -e 's/visualize/visualize/' \ + -e 's/summarize/summarize/' \ + -e 's/analyzed/analyzed/' \ + -e 's/\/analyze/' \ + -e 's/favor/favour/' \ + -e 's/visualisation/visualization/' From 671d2b7a15e84a118e08f1393724f611ab2c5dd0 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:19:06 +0200 Subject: [PATCH 20/49] run workflow on push event --- .github/workflows/american-english.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 53b97034..8d344685 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -3,6 +3,7 @@ on: branches: - devel - RELEASE_** + push: paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown"] workflow_dispatch: name: Convert British English spelling into American English spelling From 6f3cfbcf639b6eb79be0a202f29b931734ea5e6f Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:20:24 +0200 Subject: [PATCH 21/49] fix: move push event to correct place --- .github/workflows/american-english.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 8d344685..237795e2 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -3,9 +3,9 @@ on: branches: - devel - RELEASE_** - push: paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown"] workflow_dispatch: + push: name: Convert British English spelling into American English spelling permissions: read-all jobs: From e903a1f51664949d6eb721e92b4f61a755c09f00 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:21:33 +0200 Subject: [PATCH 22/49] remove git push --- .github/workflows/american-english.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 237795e2..035a0475 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -29,5 +29,5 @@ jobs: echo "No changes to commit." else git commit -m "Convert from British to American English" - git push origin HEAD:${{ github.head_ref }} + # git push origin HEAD:${{ github.head_ref }} fi From 4f4710af929d333bce03ad9e65a6633eec30fb59 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:24:00 +0200 Subject: [PATCH 23/49] add git diff --- .github/workflows/american-english.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 035a0475..b9e85c0f 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -29,5 +29,6 @@ jobs: echo "No changes to commit." else git commit -m "Convert from British to American English" + git diff HEAD~1 # git push origin HEAD:${{ github.head_ref }} fi From 890a18e4df2bb7aa640e944b8d5105eceb6a7a44 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:28:41 +0200 Subject: [PATCH 24/49] feat: use git-auto-commit action to push commits --- .github/workflows/american-english.yaml | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index b9e85c0f..5cc99963 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -21,14 +21,7 @@ jobs: - name: Convert from American English to British English run: bash .github/workflows/convert-british-to-american.sh - name: Commit and push changes - run: | - git config --local user.name "$GITHUB_ACTOR" - git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" - git add -u - if git diff --cached --quiet; then - echo "No changes to commit." - else - git commit -m "Convert from British to American English" - git diff HEAD~1 - # git push origin HEAD:${{ github.head_ref }} - fi + # Commit all changed files back to the repository + uses: stefanzweifel/git-auto-commit-action@v7 + with: + commit_message: Convert American English to British Enlish From 6bfc34a94a94a102e8989b0361dbbde98faf4b42 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:31:57 +0200 Subject: [PATCH 25/49] remove print0 from sed --- convert-british-to-american.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/convert-british-to-american.sh b/convert-british-to-american.sh index 7ff52b6d..adb785b0 100755 --- a/convert-british-to-american.sh +++ b/convert-british-to-american.sh @@ -2,7 +2,7 @@ set -e -find . -type f -print0 -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | +find . -type f -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | xargs -0 sed -i \ -e 's/visualize/visualize/' \ -e 's/summarize/summarize/' \ From 633b0f165dcc2ac1f63dae84a212bde757b9ffca Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:33:33 +0200 Subject: [PATCH 26/49] remove -O from xargs --- convert-british-to-american.sh | 2 +- inst/pages/alpha_diversity.qmd | 4 ++-- inst/pages/differential_abundance.qmd | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/convert-british-to-american.sh b/convert-british-to-american.sh index adb785b0..3c98b3c6 100755 --- a/convert-british-to-american.sh +++ b/convert-british-to-american.sh @@ -3,7 +3,7 @@ set -e find . -type f -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | - xargs -0 sed -i \ + xargs sed -i \ -e 's/visualize/visualize/' \ -e 's/summarize/summarize/' \ -e 's/analyzed/analyzed/' \ diff --git a/inst/pages/alpha_diversity.qmd b/inst/pages/alpha_diversity.qmd index 4ceb23ea..4faea66b 100644 --- a/inst/pages/alpha_diversity.qmd +++ b/inst/pages/alpha_diversity.qmd @@ -34,8 +34,8 @@ evident from their names. @bastiaanssen2023bugs1 lay out this relationship across two factors (See table below); First, alpha diversity metrics can be defined as special cases of a unifying equation of **diversity**, where the **Hill number** determines the specific index captured. Lower Hill numbers -favor **richness**, the number of distinct taxonomic features, whereas higher -numbers favor **evenness**, how the taxonomic features are distributed over +favour **richness**, the number of distinct taxonomic features, whereas higher +numbers favour **evenness**, how the taxonomic features are distributed over the sample [@Hill1973]. Second, some alpha diversity metrics are weighted based on phylogeny, like Faith's PD [-@Faith1992] and PhILR [@Silverman2017]. diff --git a/inst/pages/differential_abundance.qmd b/inst/pages/differential_abundance.qmd index 45083c2b..18197ec0 100644 --- a/inst/pages/differential_abundance.qmd +++ b/inst/pages/differential_abundance.qmd @@ -38,7 +38,7 @@ findings were also made by @Yang2022 who evaluated DAA methods 106 real datasets (along with simulated data). They found especially that on many datasets almost any taxon was detected by at least one DAA method (see Figure 7 in their article). They thus raised concerns of potential cherry-picking, that is, a -researcher would be likely to find the taxa in favor of their hypothesis by just +researcher would be likely to find the taxa in favour of their hypothesis by just trying out several different DAA methods. ## Recommendations based on recent literature {#sec-daa-recommendations} @@ -48,7 +48,7 @@ perform better compared to some of the existing alternatives. That is often achieved by employing simulated data and possibly one or more real datasets. The authors may have, however, selected their simulation models, example datasets, evaluation metrics, compared methods, etc. specifically to -show the introduced method in a favorable light. Assessing the performance of +show the introduced method in a favourable light. Assessing the performance of different methods based solely on the studies where they were originally introduced may therefore not be advisable. From 974c01e337ef1e74a05c1c38f7dedd76142ac1f6 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:43:10 +0200 Subject: [PATCH 27/49] attempt with just run --- .github/workflows/american-english.yaml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 5cc99963..c894380b 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -19,7 +19,15 @@ jobs: - name: Checkout repo uses: actions/checkout@v6 - name: Convert from American English to British English - run: bash .github/workflows/convert-british-to-american.sh + run: | + find . -type f -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | + xargs sed -i \ + -e 's/visualize/visualize/' \ + -e 's/visualisation/visualization/' \ + -e 's/summarize/summarize/' \ + -e 's/analyzed/analyzed/' \ + -e 's/\/analyze/' \ + -e 's/favor/favour/' - name: Commit and push changes # Commit all changed files back to the repository uses: stefanzweifel/git-auto-commit-action@v7 From c59aa9b67d856f65651721359d6fcec179c0bbae Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 10:50:04 +0200 Subject: [PATCH 28/49] switch favor to favour --- .github/workflows/american-english.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index c894380b..a887d5bc 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -27,7 +27,7 @@ jobs: -e 's/summarize/summarize/' \ -e 's/analyzed/analyzed/' \ -e 's/\/analyze/' \ - -e 's/favor/favour/' + -e 's/favour/favor/' - name: Commit and push changes # Commit all changed files back to the repository uses: stefanzweifel/git-auto-commit-action@v7 From 73a94fdfbd53cb3dcd4af9ff623a74d7ddea98b7 Mon Sep 17 00:00:00 2001 From: artur-sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: Fri, 16 Jan 2026 08:50:16 +0000 Subject: [PATCH 29/49] Convert American English to British Enlish --- inst/pages/alpha_diversity.qmd | 4 ++-- inst/pages/differential_abundance.qmd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/inst/pages/alpha_diversity.qmd b/inst/pages/alpha_diversity.qmd index 4faea66b..4ceb23ea 100644 --- a/inst/pages/alpha_diversity.qmd +++ b/inst/pages/alpha_diversity.qmd @@ -34,8 +34,8 @@ evident from their names. @bastiaanssen2023bugs1 lay out this relationship across two factors (See table below); First, alpha diversity metrics can be defined as special cases of a unifying equation of **diversity**, where the **Hill number** determines the specific index captured. Lower Hill numbers -favour **richness**, the number of distinct taxonomic features, whereas higher -numbers favour **evenness**, how the taxonomic features are distributed over +favor **richness**, the number of distinct taxonomic features, whereas higher +numbers favor **evenness**, how the taxonomic features are distributed over the sample [@Hill1973]. Second, some alpha diversity metrics are weighted based on phylogeny, like Faith's PD [-@Faith1992] and PhILR [@Silverman2017]. diff --git a/inst/pages/differential_abundance.qmd b/inst/pages/differential_abundance.qmd index 18197ec0..45083c2b 100644 --- a/inst/pages/differential_abundance.qmd +++ b/inst/pages/differential_abundance.qmd @@ -38,7 +38,7 @@ findings were also made by @Yang2022 who evaluated DAA methods 106 real datasets (along with simulated data). They found especially that on many datasets almost any taxon was detected by at least one DAA method (see Figure 7 in their article). They thus raised concerns of potential cherry-picking, that is, a -researcher would be likely to find the taxa in favour of their hypothesis by just +researcher would be likely to find the taxa in favor of their hypothesis by just trying out several different DAA methods. ## Recommendations based on recent literature {#sec-daa-recommendations} @@ -48,7 +48,7 @@ perform better compared to some of the existing alternatives. That is often achieved by employing simulated data and possibly one or more real datasets. The authors may have, however, selected their simulation models, example datasets, evaluation metrics, compared methods, etc. specifically to -show the introduced method in a favourable light. Assessing the performance of +show the introduced method in a favorable light. Assessing the performance of different methods based solely on the studies where they were originally introduced may therefore not be advisable. From 2d4fc386a3e57e8dfc8dbe197a33cc041ee2f4b9 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:19:32 +0200 Subject: [PATCH 30/49] use sed command directly in the workflow file --- .github/workflows/american-english.yaml | 24 +++++++++++++++++++----- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index a887d5bc..cfff7af7 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -20,14 +20,28 @@ jobs: uses: actions/checkout@v6 - name: Convert from American English to British English run: | - find . -type f -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | + find . -type f -iname "*.r" -or -iname "*.[qr]md" \ + -or -iname "*.rmarkdown" | xargs sed -i \ - -e 's/visualize/visualize/' \ + -e 's/visualise/visualize/' \ -e 's/visualisation/visualization/' \ - -e 's/summarize/summarize/' \ - -e 's/analyzed/analyzed/' \ + -e 's/summarise/summarize/' \ + -e 's/analysed/analyzed/' \ -e 's/\/analyze/' \ - -e 's/favour/favor/' + -e 's/favour/favor/' \ + -e 's/coloured/colored/' \ + -e 's/colour /color /' \ + -e 's/utilise/utilize/' \ + -e 's/maximis/maximiz/' \ + -e 's/minimis/minimiz/' \ + -e 's/normalis/normaliz/' \ + -e 's/artefact/artifact/' \ + -e 's/labelled/labeled/' \ + -e 's/behaviour/behavior/' \ + -e 's/whilst/while/' \ + -e 's/programme /program /' \ + -e 's/grey/gray/' + - name: Commit and push changes # Commit all changed files back to the repository uses: stefanzweifel/git-auto-commit-action@v7 From 82fcfc2bf66e744d4071ee7daaab86f7af688659 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:19:48 +0200 Subject: [PATCH 31/49] remove conversion bash script --- .github/workflows/convert-british-to-american.sh | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 .github/workflows/convert-british-to-american.sh diff --git a/.github/workflows/convert-british-to-american.sh b/.github/workflows/convert-british-to-american.sh deleted file mode 100644 index bd60ef58..00000000 --- a/.github/workflows/convert-british-to-american.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env bash - -set -e - -find . -type f -print0 -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | - xargs -0 sed -i \ - -e 's/visualize/visualize/' \ - -e 's/summarize/summarize/' \ - -e 's/analyzed/analyzed/' \ - -e 's/\/analyze/' \ - -e 's/favor/favor/' \ - -e 's/visualisation/visualization/' \ - -e 's/visualisation/visualization/' From 384268bd01bcfd090c9f209078c758ba1cbd44c7 Mon Sep 17 00:00:00 2001 From: artur-sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: Fri, 16 Jan 2026 09:20:01 +0000 Subject: [PATCH 32/49] Convert American English to British Enlish --- inst/pages/machine_learning.qmd | 6 +++--- inst/pages/wrangling.qmd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/inst/pages/machine_learning.qmd b/inst/pages/machine_learning.qmd index 3f339953..1ca77c4d 100644 --- a/inst/pages/machine_learning.qmd +++ b/inst/pages/machine_learning.qmd @@ -654,7 +654,7 @@ roc_p <- ggplot(data = senspec) + geom_path(aes(x = fpr, y = sensitivity, color = model)) # 1.1 Add line representing 'random guess' performance roc_p <- roc_p + - geom_abline(color = "grey30", linetype = "dashed") + geom_abline(color = "gray30", linetype = "dashed") # 1.2 Add axis titles and custom theme roc_p <- roc_p + labs(x = "FPR or (1 - Specificity)", y = "Sensitivity", title = "ROC") + @@ -666,7 +666,7 @@ prc_p <- ggplot(data = senspec) + geom_path(aes(x = sensitivity, y = precision, color = model)) # 2.1 Add line representing 'random guess' performance prc_p <- prc_p + - geom_hline(color = "grey30", linetype = "dashed", yintercept = 0.5) + geom_hline(color = "gray30", linetype = "dashed", yintercept = 0.5) # 2.2 Add axis titles and custom theme prc_p <- prc_p + labs(x = "Recall or Sensitivity", y = "Precision", title = "PRC") + @@ -765,7 +765,7 @@ table(test_data$diagnosis) obs_vs_pred <- ggplot(data = test_data) + geom_point(aes(x = pred, y = BMI, color = diagnosis), size = 2) # Add line showing perfect prediction -obs_vs_pred <- obs_vs_pred + geom_abline(color = "grey30", linetype = "dashed") +obs_vs_pred <- obs_vs_pred + geom_abline(color = "gray30", linetype = "dashed") # Make axes of same scale obs_vs_pred <- obs_vs_pred + coord_equal(xlim = c(17, 30), ylim = c(17, 30)) # Custom axes titles diff --git a/inst/pages/wrangling.qmd b/inst/pages/wrangling.qmd index 091a7403..5e15cbd1 100644 --- a/inst/pages/wrangling.qmd +++ b/inst/pages/wrangling.qmd @@ -271,7 +271,7 @@ tse %>% group_by(.cell) %>% mutate(total_counts = sum(.abundance_counts)) %>% group_by(SampleType) %>% - summarise(total_counts = mean(total_counts)) + summarize(total_counts = mean(total_counts)) ``` We can then filter samples and leverage `r BiocStyle::CRANpkg("ggplot2")` for From 3f8e6c092755d99d3fae44684c87be3f596261be Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:20:56 +0200 Subject: [PATCH 33/49] Revert "Convert American English to British Enlish" This reverts commit 384268bd01bcfd090c9f209078c758ba1cbd44c7. --- inst/pages/machine_learning.qmd | 6 +++--- inst/pages/wrangling.qmd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/inst/pages/machine_learning.qmd b/inst/pages/machine_learning.qmd index 1ca77c4d..3f339953 100644 --- a/inst/pages/machine_learning.qmd +++ b/inst/pages/machine_learning.qmd @@ -654,7 +654,7 @@ roc_p <- ggplot(data = senspec) + geom_path(aes(x = fpr, y = sensitivity, color = model)) # 1.1 Add line representing 'random guess' performance roc_p <- roc_p + - geom_abline(color = "gray30", linetype = "dashed") + geom_abline(color = "grey30", linetype = "dashed") # 1.2 Add axis titles and custom theme roc_p <- roc_p + labs(x = "FPR or (1 - Specificity)", y = "Sensitivity", title = "ROC") + @@ -666,7 +666,7 @@ prc_p <- ggplot(data = senspec) + geom_path(aes(x = sensitivity, y = precision, color = model)) # 2.1 Add line representing 'random guess' performance prc_p <- prc_p + - geom_hline(color = "gray30", linetype = "dashed", yintercept = 0.5) + geom_hline(color = "grey30", linetype = "dashed", yintercept = 0.5) # 2.2 Add axis titles and custom theme prc_p <- prc_p + labs(x = "Recall or Sensitivity", y = "Precision", title = "PRC") + @@ -765,7 +765,7 @@ table(test_data$diagnosis) obs_vs_pred <- ggplot(data = test_data) + geom_point(aes(x = pred, y = BMI, color = diagnosis), size = 2) # Add line showing perfect prediction -obs_vs_pred <- obs_vs_pred + geom_abline(color = "gray30", linetype = "dashed") +obs_vs_pred <- obs_vs_pred + geom_abline(color = "grey30", linetype = "dashed") # Make axes of same scale obs_vs_pred <- obs_vs_pred + coord_equal(xlim = c(17, 30), ylim = c(17, 30)) # Custom axes titles diff --git a/inst/pages/wrangling.qmd b/inst/pages/wrangling.qmd index 5e15cbd1..091a7403 100644 --- a/inst/pages/wrangling.qmd +++ b/inst/pages/wrangling.qmd @@ -271,7 +271,7 @@ tse %>% group_by(.cell) %>% mutate(total_counts = sum(.abundance_counts)) %>% group_by(SampleType) %>% - summarize(total_counts = mean(total_counts)) + summarise(total_counts = mean(total_counts)) ``` We can then filter samples and leverage `r BiocStyle::CRANpkg("ggplot2")` for From b4d7ae6e40dac764294be491734e845eefe6ea48 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:21:22 +0200 Subject: [PATCH 34/49] use gray with space after --- .github/workflows/american-english.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index cfff7af7..176751d0 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -40,7 +40,7 @@ jobs: -e 's/behaviour/behavior/' \ -e 's/whilst/while/' \ -e 's/programme /program /' \ - -e 's/grey/gray/' + -e 's/grey /gray /' - name: Commit and push changes # Commit all changed files back to the repository From e7e4103cf14107759445fbd76da10c1ce3a335dc Mon Sep 17 00:00:00 2001 From: artur-sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: Fri, 16 Jan 2026 09:21:38 +0000 Subject: [PATCH 35/49] Convert American English to British Enlish --- inst/pages/wrangling.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/wrangling.qmd b/inst/pages/wrangling.qmd index 091a7403..5e15cbd1 100644 --- a/inst/pages/wrangling.qmd +++ b/inst/pages/wrangling.qmd @@ -271,7 +271,7 @@ tse %>% group_by(.cell) %>% mutate(total_counts = sum(.abundance_counts)) %>% group_by(SampleType) %>% - summarise(total_counts = mean(total_counts)) + summarize(total_counts = mean(total_counts)) ``` We can then filter samples and leverage `r BiocStyle::CRANpkg("ggplot2")` for From 3399e5b18ac5372f2bb26a88d93fe92de7038f1a Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:22:22 +0200 Subject: [PATCH 36/49] Revert "Convert American English to British Enlish" This reverts commit e7e4103cf14107759445fbd76da10c1ce3a335dc. --- inst/pages/wrangling.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/wrangling.qmd b/inst/pages/wrangling.qmd index 5e15cbd1..091a7403 100644 --- a/inst/pages/wrangling.qmd +++ b/inst/pages/wrangling.qmd @@ -271,7 +271,7 @@ tse %>% group_by(.cell) %>% mutate(total_counts = sum(.abundance_counts)) %>% group_by(SampleType) %>% - summarize(total_counts = mean(total_counts)) + summarise(total_counts = mean(total_counts)) ``` We can then filter samples and leverage `r BiocStyle::CRANpkg("ggplot2")` for From 9adb212793c97bf0bc66c51cd67caa5f840c448a Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:22:47 +0200 Subject: [PATCH 37/49] remove the second conversion script --- convert-british-to-american.sh | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100755 convert-british-to-american.sh diff --git a/convert-british-to-american.sh b/convert-british-to-american.sh deleted file mode 100755 index 3c98b3c6..00000000 --- a/convert-british-to-american.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash - -set -e - -find . -type f -iname "*.r" -or -iname "*.[qr]md" -or -iname "*.[r]markdown" | - xargs sed -i \ - -e 's/visualize/visualize/' \ - -e 's/summarize/summarize/' \ - -e 's/analyzed/analyzed/' \ - -e 's/\/analyze/' \ - -e 's/favor/favour/' \ - -e 's/visualisation/visualization/' From 21327b96e377de427b1d5e56c7b95726fa84d2f2 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:23:37 +0200 Subject: [PATCH 38/49] add additional summarise replacements --- .github/workflows/american-english.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 176751d0..0a3d3315 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -25,7 +25,9 @@ jobs: xargs sed -i \ -e 's/visualise/visualize/' \ -e 's/visualisation/visualization/' \ - -e 's/summarise/summarize/' \ + -e 's/summarise /summarize /' \ + -e 's/summarised /summarized /' \ + -e 's/summarises /summarizes /' \ -e 's/analysed/analyzed/' \ -e 's/\/analyze/' \ -e 's/favour/favor/' \ From 18698c4763f44c801ee5d20f38d3f7049060ecbe Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Fri, 16 Jan 2026 11:24:40 +0200 Subject: [PATCH 39/49] remove github action trigger on push --- .github/workflows/american-english.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 0a3d3315..9e790255 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -5,7 +5,6 @@ on: - RELEASE_** paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown"] workflow_dispatch: - push: name: Convert British English spelling into American English spelling permissions: read-all jobs: From f548da7e2e21747ad6f46025ba14585aaf97cf43 Mon Sep 17 00:00:00 2001 From: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Date: Thu, 22 Jan 2026 08:45:17 +0200 Subject: [PATCH 40/49] Testing American English GHA --- inst/pages/extra_material/add-comm-typing.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index 86ece7b6..c43ce53c 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -40,7 +40,7 @@ km <- kmeans(diss, 2, nstart = 25) # Add the result to colData colData(tse)$clusters <- as.factor(km$cluster) -# Perform PCoA so that we can visualize clusters +# Perform PCoA so that we can visualise clusters tse <- addMDS(tse, assay.type = "relabundance", FUN = vegan::vegdist, method = "bray") From 0c8f50c4921d3b8912c490fa125f99f1b137ac0b Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 22 Jan 2026 11:01:34 +0200 Subject: [PATCH 41/49] feat(workflows): add branch checkout to actions/checkout This avoids checking out the repo in a detached state. See https://github.com/stefanzweifel/git-auto-commit-action?tab=readme-ov-file#checkout-the-correct-branch for more info. --- .github/workflows/american-english.yaml | 2 ++ .github/workflows/style.yaml | 1 + 2 files changed, 3 insertions(+) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 9e790255..d8015d90 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -17,6 +17,8 @@ jobs: steps: - name: Checkout repo uses: actions/checkout@v6 + with: + ref: ${{ github.head_ref }} - name: Convert from American English to British English run: | find . -type f -iname "*.r" -or -iname "*.[qr]md" \ diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index 667e6446..fee80b93 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -19,6 +19,7 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: 0 + ref: ${{ github.head_ref }} - name: Setup R uses: r-lib/actions/setup-r@v2 with: From b1219ee363e10a931f048756fdbe3e99e12ab092 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 22 Jan 2026 11:03:13 +0200 Subject: [PATCH 42/49] chore: styling of style.yaml --- .github/workflows/style.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index fee80b93..0c993ef4 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -3,7 +3,14 @@ on: branches: - devel - RELEASE_** - paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"] + paths: + [ + "**.[rR]", + "**.[qrR]md", + "**.[rR]markdown", + "**.[rR]nw", + "**.[rR]profile", + ] workflow_dispatch: name: Style code permissions: read-all From 23a28b62e0d893c1b433d62c2fc773392aa45bfc Mon Sep 17 00:00:00 2001 From: artur-sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: Thu, 22 Jan 2026 09:08:26 +0000 Subject: [PATCH 43/49] Convert American English to British Enlish --- inst/pages/extra_material/add-comm-typing.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/extra_material/add-comm-typing.Rmd b/inst/pages/extra_material/add-comm-typing.Rmd index c43ce53c..86ece7b6 100644 --- a/inst/pages/extra_material/add-comm-typing.Rmd +++ b/inst/pages/extra_material/add-comm-typing.Rmd @@ -40,7 +40,7 @@ km <- kmeans(diss, 2, nstart = 25) # Add the result to colData colData(tse)$clusters <- as.factor(km$cluster) -# Perform PCoA so that we can visualise clusters +# Perform PCoA so that we can visualize clusters tse <- addMDS(tse, assay.type = "relabundance", FUN = vegan::vegdist, method = "bray") From 2c22d48f3d46ce53229ecc03acafad5100930c9e Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 22 Jan 2026 11:21:21 +0200 Subject: [PATCH 44/49] fix(workflow): checkout HEAD of the current pull request --- .github/workflows/american-english.yaml | 3 ++- .github/workflows/style.yaml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index d8015d90..71cc0c42 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -18,7 +18,8 @@ jobs: - name: Checkout repo uses: actions/checkout@v6 with: - ref: ${{ github.head_ref }} + fetch-depth: 0 + ref: ${{ github.event.pull_request.head.ref }} - name: Convert from American English to British English run: | find . -type f -iname "*.r" -or -iname "*.[qr]md" \ diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index 0c993ef4..b1cbe9d1 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -26,7 +26,7 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: 0 - ref: ${{ github.head_ref }} + ref: ${{ github.event.pull_request.head.ref }} - name: Setup R uses: r-lib/actions/setup-r@v2 with: From 4def9cc129730a5e5d2c6a168d207eb859624101 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 22 Jan 2026 11:29:13 +0200 Subject: [PATCH 45/49] remove fetch from checkout action --- .github/workflows/style.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index b1cbe9d1..d9f39525 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -26,7 +26,6 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: 0 - ref: ${{ github.event.pull_request.head.ref }} - name: Setup R uses: r-lib/actions/setup-r@v2 with: From 9acc2b2c05b3b4bb6d9fa34fb0e63df939197263 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Thu, 22 Jan 2026 11:31:42 +0200 Subject: [PATCH 46/49] remove fetch from checkout action --- .github/workflows/american-english.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index 71cc0c42..cb4fad5e 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -19,7 +19,6 @@ jobs: uses: actions/checkout@v6 with: fetch-depth: 0 - ref: ${{ github.event.pull_request.head.ref }} - name: Convert from American English to British English run: | find . -type f -iname "*.r" -or -iname "*.[qr]md" \ From 25dcdb195f8f1f4f1c56dd8ecaab3c6c7a2d23a1 Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Mon, 9 Feb 2026 17:01:55 +0200 Subject: [PATCH 47/49] feat: submit updates to summarise* substitutions --- .github/workflows/american-english.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml index cb4fad5e..3fa51ebf 100644 --- a/.github/workflows/american-english.yaml +++ b/.github/workflows/american-english.yaml @@ -23,11 +23,11 @@ jobs: run: | find . -type f -iname "*.r" -or -iname "*.[qr]md" \ -or -iname "*.rmarkdown" | - xargs sed -i \ + xargs sed -E -i \ -e 's/visualise/visualize/' \ -e 's/visualisation/visualization/' \ - -e 's/summarise /summarize /' \ - -e 's/summarised /summarized /' \ + -e 's/\([^(])/summarize\1/' \ + -e 's/\([^(])/summarized\1/' \ -e 's/summarises /summarizes /' \ -e 's/analysed/analyzed/' \ -e 's/\/analyze/' \ From a86df6f52e2fe4a5cb137f8b2547707bff0a1aab Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Wed, 11 Feb 2026 15:14:28 +0200 Subject: [PATCH 48/49] remove gha --- .github/workflows/american-english.yaml | 52 ------------------------- 1 file changed, 52 deletions(-) delete mode 100644 .github/workflows/american-english.yaml diff --git a/.github/workflows/american-english.yaml b/.github/workflows/american-english.yaml deleted file mode 100644 index 3fa51ebf..00000000 --- a/.github/workflows/american-english.yaml +++ /dev/null @@ -1,52 +0,0 @@ -on: - pull_request: - branches: - - devel - - RELEASE_** - paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown"] - workflow_dispatch: -name: Convert British English spelling into American English spelling -permissions: read-all -jobs: - convert: - runs-on: ubuntu-latest - permissions: - contents: write - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - name: Checkout repo - uses: actions/checkout@v6 - with: - fetch-depth: 0 - - name: Convert from American English to British English - run: | - find . -type f -iname "*.r" -or -iname "*.[qr]md" \ - -or -iname "*.rmarkdown" | - xargs sed -E -i \ - -e 's/visualise/visualize/' \ - -e 's/visualisation/visualization/' \ - -e 's/\([^(])/summarize\1/' \ - -e 's/\([^(])/summarized\1/' \ - -e 's/summarises /summarizes /' \ - -e 's/analysed/analyzed/' \ - -e 's/\/analyze/' \ - -e 's/favour/favor/' \ - -e 's/coloured/colored/' \ - -e 's/colour /color /' \ - -e 's/utilise/utilize/' \ - -e 's/maximis/maximiz/' \ - -e 's/minimis/minimiz/' \ - -e 's/normalis/normaliz/' \ - -e 's/artefact/artifact/' \ - -e 's/labelled/labeled/' \ - -e 's/behaviour/behavior/' \ - -e 's/whilst/while/' \ - -e 's/programme /program /' \ - -e 's/grey /gray /' - - - name: Commit and push changes - # Commit all changed files back to the repository - uses: stefanzweifel/git-auto-commit-action@v7 - with: - commit_message: Convert American English to British Enlish From 810bffad6ad958d012a9612588f04790025a15ed Mon Sep 17 00:00:00 2001 From: Artur Sannikov Date: Wed, 11 Feb 2026 15:23:27 +0200 Subject: [PATCH 49/49] chore: revert style yaml to its devel state --- .github/workflows/style.yaml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index d9f39525..667e6446 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -3,14 +3,7 @@ on: branches: - devel - RELEASE_** - paths: - [ - "**.[rR]", - "**.[qrR]md", - "**.[rR]markdown", - "**.[rR]nw", - "**.[rR]profile", - ] + paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"] workflow_dispatch: name: Style code permissions: read-all