From 613011c8953d1dcbbedd4a2d1d8036071104f65f Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Fri, 14 Jun 2024 13:01:20 -0700 Subject: [PATCH 1/7] bug fix to address #55 --- DESCRIPTION | 4 ++-- NEWS.md | 4 ++++ R/bayesian_graphical_clustering.R | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 61d620a..a76943a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Type: Package Package: MotrpacRatTraining6mo Title: Analysis of the MoTrPAC endurance exercise training data in 6-month-old rats -Version: 1.6.5 +Version: 1.6.6 Authors@R: c( person("Nicole", "Gay", , "nicole.r.gay@gmail.com", role = c("cre", "aut")), person("David", "Amar", , "ddam.am@gmail.com", role = "aut"), @@ -29,7 +29,7 @@ Imports: dplyr, edgeR, ggplot2, - ggraph, + ggraph (>= 2.2.0), grid, igraph, limma, diff --git a/NEWS.md b/NEWS.md index 5b83a45..cc62b97 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# MotrpacRatTraining6mo 1.6.6 (2024-06-14) + +* Fix bug due to backwards incompatibility between `ggraph` 2.1.0 and 2.2.0. Require `ggraph >= 2.2.0`. + # MotrpacRatTraining6mo 1.6.5 (2023-11-08) * Point to development version of `RCy3` from GitHub to avoid `R-CMD check` error `RCy3: Can't install dependency uchardet`. diff --git a/R/bayesian_graphical_clustering.R b/R/bayesian_graphical_clustering.R index af2285a..e91285f 100644 --- a/R/bayesian_graphical_clustering.R +++ b/R/bayesian_graphical_clustering.R @@ -922,7 +922,7 @@ get_tree_plot_for_tissue <- function( d_g_our_layout[grepl(n,d_g_our_layout$name),"y"] = l_y_lim[1] + (j-1)*yjump } # make sure that the 0w node is in the same line as of the no response - d_g_our_layout[d_g_our_layout$name == "0w","y"] = d_g_our_layout[grepl("F0_M0",d_g_our_layout$name),"y"][1] + d_g_our_layout[d_g_our_layout$name == "0w","y"] = d_g_our_layout[grepl("F0_M0",d_g_our_layout$name),"y"][1,1] # set node sizes and other features igraph::V(d_g)$setsize = d_nodes[V(d_g)$name,"size"] igraph::V(d_g)$setsize[V(d_g)$name == "0w"] = stats::median(igraph::V(d_g)$setsize) From c64e1b830c3ada0be12608d88e417166911d0ff7 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Sun, 29 Sep 2024 19:06:59 -0700 Subject: [PATCH 2/7] trigger actions From 1cca9f08202c7cf6faa15be9bb55f5d39d0575f1 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Sun, 29 Sep 2024 19:18:14 -0700 Subject: [PATCH 3/7] replace preprint with nature pub --- README.md | 7 +++---- _pkgdown.yml | 4 ++-- vignettes/MotrpacRatTraining6mo.Rmd | 14 +++++++------- vignettes/key_metabolites.Rmd | 2 +- 4 files changed, 13 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 69f7dfd..e7e5297 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ This package provides functions to fetch, explore, and reproduce the processed d analysis results presented in the main paper for the first large-scale multi-omic multi-tissue endurance exercise training study conducted in young adult rats by the Molecular Transducers of Physical Activity Consortium -(MoTrPAC). Find the [preprint on bioRxiv](https://www.biorxiv.org/content/10.1101/2022.09.21.508770v2). +(MoTrPAC). See our publication in [*Nature*](https://www.nature.com/articles/s41586-023-06877-w). **See the [vignette](https://motrpac.github.io/MotrpacRatTraining6mo/articles/MotrpacRatTraining6mo.html) for examples of how to use this package.** While some of the functions in this package can be used by themselves, they @@ -104,6 +104,5 @@ Specific datasets used are [version numbers]. * Data used in the preparation of this article were obtained from the Molecular Transducers of Physical Activity Consortium (MoTrPAC) MotrpacRatTraining6moData R package [version number]. -## Citing MoTrPAC data -MoTrPAC Study Group. 2022. Temporal dynamics of the multi-omic response to endurance exercise training across tissues. -bioRxiv doi: 10.1101/2022.09.21.508770 +## Citing MoTrPAC data +MoTrPAC Study Group. Temporal dynamics of the multi-omic response to endurance exercise training. *Nature* **629**, 174–183 (2024). https://doi.org/10.1038/s41586-023-06877-w diff --git a/_pkgdown.yml b/_pkgdown.yml index 2c859d1..372d0d7 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,8 +4,8 @@ template: home: links: - - text: Preprint - href: https://www.biorxiv.org/content/10.1101/2022.09.21.508770v2 + - text: Publications + href: https://www.nature.com/collections/cfiiibcebh reference: diff --git a/vignettes/MotrpacRatTraining6mo.Rmd b/vignettes/MotrpacRatTraining6mo.Rmd index 4e39395..36d2b21 100644 --- a/vignettes/MotrpacRatTraining6mo.Rmd +++ b/vignettes/MotrpacRatTraining6mo.Rmd @@ -74,7 +74,7 @@ This package provides functions to fetch, explore, and reproduce the processed data and downstream analysis results presented in the main paper for the first large-scale multi-omic multi-tissue endurance exercise training study conducted in young adult rats by the Molecular Transducers of Physical Activity Consortium -(MoTrPAC). Find the [preprint on bioRxiv](https://www.biorxiv.org/content/10.1101/2022.09.21.508770v2). +(MoTrPAC). See our publication in [*Nature*](https://www.nature.com/articles/s41586-023-06877-w). **We highly recommend skimming the preprint before using this package as it provides important context and much greater detail than we can provide here.** @@ -151,7 +151,7 @@ e.g., [`?METAB_FEATURE_ID_MAP`](https://motrpac.github.io/MotrpacRatTraining6moD ## Study design -Details of the experimental design can be found in the [supplementary methods of the bioRxiv preprint](https://www.biorxiv.org/content/biorxiv/early/2022/10/05/2022.09.21.508770/DC1/embed/media-1.pdf?download=true). +Details of the experimental design can be found in the [supplementary information of our *Nature* publication](https://www.nature.com/articles/s41586-023-06877-w#Sec14). Briefly, 6-month-old young adult rats were subjected to progressive endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last training bout. @@ -355,7 +355,7 @@ and you can load data objects into your environment using `data()`, e.g., ## Differential analysis More details about the differential analysis methods are available in the -[supplementary methods of the bioRxiv preprint](https://www.biorxiv.org/content/biorxiv/early/2022/10/05/2022.09.21.508770/DC1/embed/media-1.pdf?download=true). +[supplementary information of our *Nature* publication](https://www.nature.com/articles/s41586-023-06877-w#Sec14). Simply put, the *training* differential analysis considers all training groups for each sex (sedentary controls and 4 training time points) to determine if the analyte significantly changes in either @@ -501,7 +501,7 @@ run `repfdr` on your own data, and explore and visualize the nodes, edges, and p (collectively referred to as clusters) in the resulting graph. For additional details and advantages of this approach over traditional clustering methods, see the -[supplementary methods of the bioRxiv preprint](https://www.biorxiv.org/content/biorxiv/early/2022/10/05/2022.09.21.508770/DC1/embed/media-1.pdf?download=true). +[supplementary information of our *Nature* publication](https://www.nature.com/articles/s41586-023-06877-w#Sec14). If you are more interested in exploring the existing pathway enrichment results, skip to [Visualization of pathway enrichment results](#vizEnrich). @@ -582,7 +582,7 @@ hist(unlist(lapply(paths, length)), breaks=100) ``` `extract_main_clusters()` returns the subset of graphical clusters for which pathway -enrichment was performed for the [preprint](https://www.biorxiv.org/content/10.1101/2022.09.21.508770v2), +enrichment was performed for the [*Nature* publication](https://www.nature.com/articles/s41586-023-06877-w), namely the 2 largest nodes, 2 largest edges, 10 largest non-null paths, and all 8-week nodes from the graphical representation of training-regulated features in each tissue. ```{r extract main clusters} @@ -753,8 +753,8 @@ artificially small p-values. Pathway enrichment results were adjusted over *all* tests using [IHW](https://www.nature.com/articles/nmeth.3885) with tissue as a covariate. -Pathway enrichment results for graphical clusters of interest presented in the -[preprint](https://www.biorxiv.org/content/10.1101/2022.09.21.508770v2) are provided in `GRAPH_PW_ENRICH`. +Pathway enrichment results for graphical clusters of interest presented in our +[publication](https://www.nature.com/articles/s41586-023-06877-w) are provided in `GRAPH_PW_ENRICH`. ### Enrichment with standard PWs `cluster_pathway_enrichment()` is a wrapper for diff --git a/vignettes/key_metabolites.Rmd b/vignettes/key_metabolites.Rmd index 99c0164..fea85be 100644 --- a/vignettes/key_metabolites.Rmd +++ b/vignettes/key_metabolites.Rmd @@ -38,7 +38,7 @@ knitr::opts_chunk$set( ## Motivation -This report was motivated by this reviewer comment regarding the [preprint](https://www.biorxiv.org/content/10.1101/2022.09.21.508770v2): +This report was motivated by this reviewer comment regarding our [Nature publication](https://www.nature.com/articles/s41586-023-06877-w): **Reviewer 1:** Given the extensive collection of metabolomics data (targeted and untargeted) for so many tissues and temporal timepoints (Figure 1C) it will be interesting to explore the changes of several key cellular metabolites in addition to the KEGG pathways. For example, it will be interesting to see sex- and time-specific changes in the plasma, muscles, heart of such metabolites as glucose, pyruvate, lactate, acetate, perhaps key intermediates of glycolysis and the TCA cycle. If the data is available, it will be also interesting to characterize the changes in the energy and redox ratios, i.e. ATP/ADP, NADH/NAD+ (or individual concentrations, such as ATP). Given the central roles of these metabolites in cellular physiology/health and multiple changes in the corresponding metabolic pathways (Figure 7), it will be good to present and discuss the observed metabolic changes. From 274baa43b13f44878850f5ea2f1104b3239acc2c Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Sun, 29 Sep 2024 19:21:38 -0700 Subject: [PATCH 4/7] italicize --- vignettes/key_metabolites.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/key_metabolites.Rmd b/vignettes/key_metabolites.Rmd index fea85be..03d642b 100644 --- a/vignettes/key_metabolites.Rmd +++ b/vignettes/key_metabolites.Rmd @@ -38,7 +38,7 @@ knitr::opts_chunk$set( ## Motivation -This report was motivated by this reviewer comment regarding our [Nature publication](https://www.nature.com/articles/s41586-023-06877-w): +This report was motivated by this reviewer comment regarding our [*Nature* publication](https://www.nature.com/articles/s41586-023-06877-w): **Reviewer 1:** Given the extensive collection of metabolomics data (targeted and untargeted) for so many tissues and temporal timepoints (Figure 1C) it will be interesting to explore the changes of several key cellular metabolites in addition to the KEGG pathways. For example, it will be interesting to see sex- and time-specific changes in the plasma, muscles, heart of such metabolites as glucose, pyruvate, lactate, acetate, perhaps key intermediates of glycolysis and the TCA cycle. If the data is available, it will be also interesting to characterize the changes in the energy and redox ratios, i.e. ATP/ADP, NADH/NAD+ (or individual concentrations, such as ATP). Given the central roles of these metabolites in cellular physiology/health and multiple changes in the corresponding metabolic pathways (Figure 7), it will be good to present and discuss the observed metabolic changes. From 2750b996568e8c758e4d929e5b98092ffd3f0c2f Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Sun, 29 Sep 2024 19:23:23 -0700 Subject: [PATCH 5/7] formatting --- NEWS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index cc62b97..b8c398b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,11 +1,11 @@ -# MotrpacRatTraining6mo 1.6.6 (2024-06-14) +# MotrpacRatTraining6mo 1.6.6 (2024-09-29) * Fix bug due to backwards incompatibility between `ggraph` 2.1.0 and 2.2.0. Require `ggraph >= 2.2.0`. # MotrpacRatTraining6mo 1.6.5 (2023-11-08) * Point to development version of `RCy3` from GitHub to avoid `R-CMD check` error `RCy3: Can't install dependency uchardet`. -* Install `plotrix` from GitHub instead of CRAN to avoid `R-CMD check` warning `Requires (indirectly) orphaned package: ‘plotrix’`. +* Install `plotrix` from GitHub instead of CRAN to avoid `R-CMD check` warning `Requires (indirectly) orphaned package: 'plotrix'`. CRAN has marked `plotrix` as orphaned. `plotrix` is a dependency for `mutoss`, which is a dependency for `metap`. * Increment required `MotrpacRatTraining6moData` version. From bf4aea27594db65b0eddeb18a158bdbac5b17cb0 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Sun, 29 Sep 2024 19:27:04 -0700 Subject: [PATCH 6/7] replace 'preprint' with 'paper' --- _pkgdown.yml | 2 +- vignettes/MotrpacRatTraining6mo.Rmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 372d0d7..5d1d8c4 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -11,7 +11,7 @@ home: reference: - title: Load data - desc: Load data and analysis results used in the preprint + desc: Load data and analysis results used in the publication contents: - list_available_data diff --git a/vignettes/MotrpacRatTraining6mo.Rmd b/vignettes/MotrpacRatTraining6mo.Rmd index 36d2b21..7d95b0e 100644 --- a/vignettes/MotrpacRatTraining6mo.Rmd +++ b/vignettes/MotrpacRatTraining6mo.Rmd @@ -75,7 +75,7 @@ data and downstream analysis results presented in the main paper for the first large-scale multi-omic multi-tissue endurance exercise training study conducted in young adult rats by the Molecular Transducers of Physical Activity Consortium (MoTrPAC). See our publication in [*Nature*](https://www.nature.com/articles/s41586-023-06877-w). -**We highly recommend skimming the preprint +**We highly recommend skimming the paper before using this package as it provides important context and much greater detail than we can provide here.** From 572dbc2c15b11345d6748512b7aeb3acb5aa0d95 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Sun, 29 Sep 2024 19:40:03 -0700 Subject: [PATCH 7/7] fix figure number reference --- vignettes/key_metabolites.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/key_metabolites.Rmd b/vignettes/key_metabolites.Rmd index 03d642b..9abc374 100644 --- a/vignettes/key_metabolites.Rmd +++ b/vignettes/key_metabolites.Rmd @@ -40,7 +40,7 @@ knitr::opts_chunk$set( This report was motivated by this reviewer comment regarding our [*Nature* publication](https://www.nature.com/articles/s41586-023-06877-w): -**Reviewer 1:** Given the extensive collection of metabolomics data (targeted and untargeted) for so many tissues and temporal timepoints (Figure 1C) it will be interesting to explore the changes of several key cellular metabolites in addition to the KEGG pathways. For example, it will be interesting to see sex- and time-specific changes in the plasma, muscles, heart of such metabolites as glucose, pyruvate, lactate, acetate, perhaps key intermediates of glycolysis and the TCA cycle. If the data is available, it will be also interesting to characterize the changes in the energy and redox ratios, i.e. ATP/ADP, NADH/NAD+ (or individual concentrations, such as ATP). Given the central roles of these metabolites in cellular physiology/health and multiple changes in the corresponding metabolic pathways (Figure 7), it will be good to present and discuss the observed metabolic changes. +**Reviewer 1:** Given the extensive collection of metabolomics data (targeted and untargeted) for so many tissues and temporal timepoints (Figure 1C) it will be interesting to explore the changes of several key cellular metabolites in addition to the KEGG pathways. For example, it will be interesting to see sex- and time-specific changes in the plasma, muscles, heart of such metabolites as glucose, pyruvate, lactate, acetate, perhaps key intermediates of glycolysis and the TCA cycle. If the data is available, it will be also interesting to characterize the changes in the energy and redox ratios, i.e. ATP/ADP, NADH/NAD+ (or individual concentrations, such as ATP). Given the central roles of these metabolites in cellular physiology/health and multiple changes in the corresponding metabolic pathways ([Figure 6]), it will be good to present and discuss the observed metabolic changes. ```{r setup, message = FALSE, warning = FALSE} library(MotrpacRatTraining6mo)