fix vignettes

pcastellanoescuder · Dec 14, 2023 · f312208 · f312208
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: POMA
 Title: Tools for Omics Data Analysis   
-Version: 1.13.3
+Version: 1.13.4
 Authors@R: 
     c(person(given = "Pol",
              family = "Castellano-Escuder",
@@ -70,6 +70,7 @@ Suggests:
     BiocStyle,
     covr,
     ggraph,
+    ggtext,
     knitr,
     patchwork,
     plotly,

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# POMA 1.13.3
+# POMA 1.13.4
 
 * New POMA theme and colorblind-friendly palette
 * Available sample normalization (sum and quantile)

diff --git a/README.Rmd b/README.Rmd
@@ -16,50 +16,49 @@ output: github_document
 | _BioC_ branch 	| Status 	| Version 	| Dependencies 	| Rank 	|
 |-	|-	|-	|-	|-	|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) 	| [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) 	| [![BioC released version](https://img.shields.io/badge/release%20version-1.6.0-blue.svg)](https://www.bioconductor.org/packages/POMA) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.3-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.4-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
 
   <!-- badges: end -->
 
 The `POMA` package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, `POMA` leverages the standardized `SummarizedExperiment` class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making `POMA` an essential asset for researchers handling omics datasets.   
 
-<!-- For more information and to get started, visit the POMA website.  -->
-
 <!-- POMA provides two different Shiny apps both for exploratory data analysis and statistical analysis that implement all POMA functions in two user-friendly web interfaces.      -->
 
 <!--   - **POMAShiny**: Shiny version of this package. https://github.com/pcastellanoescuder/POMAShiny   -->
 <!--   - **POMAcounts**: Shiny version for exploratory and statistical analysis of mass spectrometry spectral counts data and RNAseq data. https://github.com/pcastellanoescuder/POMAcounts    -->
 
-<!-- The [GitHub page](https://github.com/pcastellanoescuder/POMA) is for active development, issue tracking and forking/pulling purposes. To get an overview of the package, see the [*POMA Workflow*](https://pcastellanoescuder.github.io/POMA/articles/POMA-demo.html) vignette.      -->
-
 ## Installation
 
-To install the Bioconductor version:
+To install the Bioconductor last release version:
 
 ```{r, eval = FALSE}
 # install.packages("BiocManager")
 BiocManager::install("POMA")
 ```
 
-If you need the GitHub version (not recommended), use:
+To install the GitHub devel version:
 
 ```{r, eval = FALSE}
 # install.packages("devtools")
-devtools::install_github("pcastellanoescuder/POMA")
+devtools::install_github("pcastellanoescuder/POMA", ref = "devel")
 ```
 
 ## Citation
 
-Castellano-Escuder et al. POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis. PLoS Comput Biol. 2021 Jul 1;17(7):e1009148. doi: 10.1371/journal.pcbi.1009148. PMID: 34197462; PMCID: PMC8279420.
-
-<!-- ### Cited In -->
-
-<!-- Bellio C, Emperador M, Castellano P, et al. GDF15 Is an Eribulin Response Biomarker also Required for Survival of DTP Breast Cancer Cells. Cancers (Basel). 2022 May 23;14(10):2562. doi: 10.3390/cancers14102562. PMID: 35626166; PMCID: PMC9139899. -->
-
-<!-- González-Domínguez R, Castellano-Escuder P, Lefèvre-Arbogast S, et al. Apolipoprotein E and sex modulate fatty acid metabolism in a prospective observational study of cognitive decline. Alzheimers Res Ther. 2022 Jan 3;14(1):1. doi: 10.1186/s13195-021-00948-8. PMID: 34980257; PMCID: PMC8725342. -->
-
-<!-- González-Domínguez R, Castellano-Escuder P, Carmona F, et al. Food and Microbiota Metabolites Associate with Cognitive Decline in Older Subjects: A 12-Year Prospective Study. Mol Nutr Food Res. 2021 Dec;65(23):e2100606. doi: 10.1002/mnfr.202100606. Epub 2021 Oct 28. PMID: 34661340. -->
-
-<!-- Peron G, Gargari G, Meroño T, et al. Crosstalk among intestinal barrier, gut microbiota and serum metabolome after a polyphenol-rich diet in older subjects with "leaky gut": The MaPLE trial. Clin Nutr. 2021 Oct;40(10):5288-5297. doi: 10.1016/j.clnu.2021.08.027. Epub 2021 Sep 9. PMID: 34534897. -->
+Castellano-Escuder et al. POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis. _PLoS Comput Biol._ 2021 Jul 1;17(7):e1009148. doi: 10.1371/journal.pcbi.1009148. PMID: 34197462; PMCID: PMC8279420.
+
+```{bibtex}
+@article{castellano2021pomashiny,
+  title={POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis},
+  author={Castellano-Escuder, Pol and Gonz{\'a}lez-Dom{\'\i}nguez, Ra{\'u}l and Carmona-Pontaque, Francesc and Andr{\'e}s-Lacueva, Cristina and S{\'a}nchez-Pla, Alex},
+  journal={PLOS Computational Biology},
+  volume={17},
+  number={7},
+  pages={e1009148},
+  year={2021},
+  publisher={Public Library of Science San Francisco, CA USA}
+}
+```
 
 ## News
 

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li
 | *BioC* branch                                                           | Status                                                                                                                                                  | Version                                                                                                                                            | Dependencies                                                                                                                                         | Rank                                                                                                                         |
 |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.6.0-blue.svg)](https://www.bioconductor.org/packages/POMA)              | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.3-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since)     | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.4-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since)     | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
 
 <!-- badges: end -->
 
@@ -33,40 +33,45 @@ Bioconductor tools. This approach guarantees maximum flexibility and
 replicability, making `POMA` an essential asset for researchers handling
 omics datasets.
 
-<!-- For more information and to get started, visit the POMA website.  -->
 <!-- POMA provides two different Shiny apps both for exploratory data analysis and statistical analysis that implement all POMA functions in two user-friendly web interfaces.      -->
 <!--   - **POMAShiny**: Shiny version of this package. https://github.com/pcastellanoescuder/POMAShiny   -->
 <!--   - **POMAcounts**: Shiny version for exploratory and statistical analysis of mass spectrometry spectral counts data and RNAseq data. https://github.com/pcastellanoescuder/POMAcounts    -->
-<!-- The [GitHub page](https://github.com/pcastellanoescuder/POMA) is for active development, issue tracking and forking/pulling purposes. To get an overview of the package, see the [*POMA Workflow*](https://pcastellanoescuder.github.io/POMA/articles/POMA-demo.html) vignette.      -->
 
 ## Installation
 
-To install the Bioconductor version:
+To install the Bioconductor last release version:
 
 ``` r
 # install.packages("BiocManager")
 BiocManager::install("POMA")
 ```
 
-If you need the GitHub version (not recommended), use:
+To install the GitHub devel version:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("pcastellanoescuder/POMA")
+devtools::install_github("pcastellanoescuder/POMA", ref = "devel")
 ```
 
 ## Citation
 
 Castellano-Escuder et al. POMAShiny: A user-friendly web-based workflow
-for metabolomics and proteomics data analysis. PLoS Comput Biol. 2021
+for metabolomics and proteomics data analysis. *PLoS Comput Biol.* 2021
 Jul 1;17(7):e1009148. doi: 10.1371/journal.pcbi.1009148. PMID: 34197462;
 PMCID: PMC8279420.
 
-<!-- ### Cited In -->
-<!-- Bellio C, Emperador M, Castellano P, et al. GDF15 Is an Eribulin Response Biomarker also Required for Survival of DTP Breast Cancer Cells. Cancers (Basel). 2022 May 23;14(10):2562. doi: 10.3390/cancers14102562. PMID: 35626166; PMCID: PMC9139899. -->
-<!-- González-Domínguez R, Castellano-Escuder P, Lefèvre-Arbogast S, et al. Apolipoprotein E and sex modulate fatty acid metabolism in a prospective observational study of cognitive decline. Alzheimers Res Ther. 2022 Jan 3;14(1):1. doi: 10.1186/s13195-021-00948-8. PMID: 34980257; PMCID: PMC8725342. -->
-<!-- González-Domínguez R, Castellano-Escuder P, Carmona F, et al. Food and Microbiota Metabolites Associate with Cognitive Decline in Older Subjects: A 12-Year Prospective Study. Mol Nutr Food Res. 2021 Dec;65(23):e2100606. doi: 10.1002/mnfr.202100606. Epub 2021 Oct 28. PMID: 34661340. -->
-<!-- Peron G, Gargari G, Meroño T, et al. Crosstalk among intestinal barrier, gut microbiota and serum metabolome after a polyphenol-rich diet in older subjects with "leaky gut": The MaPLE trial. Clin Nutr. 2021 Oct;40(10):5288-5297. doi: 10.1016/j.clnu.2021.08.027. Epub 2021 Sep 9. PMID: 34534897. -->
+``` bibtex
+@article{castellano2021pomashiny,
+  title={POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis},
+  author={Castellano-Escuder, Pol and Gonz{\'a}lez-Dom{\'\i}nguez, Ra{\'u}l and Carmona-Pontaque, Francesc and Andr{\'e}s-Lacueva, Cristina and S{\'a}nchez-Pla, Alex},
+  journal={PLOS Computational Biology},
+  volume={17},
+  number={7},
+  pages={e1009148},
+  year={2021},
+  publisher={Public Library of Science San Francisco, CA USA}
+}
+```
 
 ## News
 

diff --git a/vignettes/POMA-normalization.Rmd b/vignettes/POMA-normalization.Rmd
@@ -19,7 +19,7 @@ link-citations: true
 
 **Compiled date**: `r Sys.Date()`
 
-**Last edited**: 2023-12-07
+**Last edited**: 2023-12-14
 
 **License**: `r packageDescription("POMA")[["License"]]`
 
@@ -44,6 +44,7 @@ BiocManager::install("POMA")
 
 ```{r, warning = FALSE, message = FALSE, comment = FALSE}
 library(POMA)
+library(ggtext)
 library(patchwork)
 ```
 

diff --git a/vignettes/POMA-workflow.Rmd b/vignettes/POMA-workflow.Rmd
@@ -19,7 +19,7 @@ link-citations: true
 
 **Compiled date**: `r Sys.Date()`
 
-**Last edited**: 2023-12-07
+**Last edited**: 2023-12-14
 
 **License**: `r packageDescription("POMA")[["License"]]`
 
@@ -44,6 +44,7 @@ BiocManager::install("POMA")
 
 ```{r, warning = FALSE, message = FALSE}
 library(POMA)
+library(ggtext)
 ```
 
 # The POMA Workflow
@@ -114,25 +115,21 @@ normalized
 <!-- `PomaBoxplots` generates boxplots for all samples or features of a `SummarizedExperiment` object. Here, we can compare objects before and after normalization step.     -->
 
 ```{r, message = FALSE}
-PomaBoxplots(imputed, 
-             x = "samples") # data before normalization
+PomaBoxplots(imputed, x = "samples") # data before normalization
 ```
 
 ```{r, message = FALSE}
-PomaBoxplots(normalized, 
-             x = "samples") # data after normalization
+PomaBoxplots(normalized, x = "samples") # data after normalization
 ```
 
 <!-- On the other hand, `PomaDensity` shows the distribution of all features before and after the normalization process.     -->
 
 ```{r, message = FALSE}
-PomaDensity(imputed, 
-            x = "features") # data before normalization
+PomaDensity(imputed, x = "features") # data before normalization
 ```
 
 ```{r, message = FALSE}
-PomaDensity(normalized, 
-            x = "features") # data after normalization
+PomaDensity(normalized, x = "features") # data after normalization
 ```
 
 ### Outlier Detection