1. POMA
  2. Commit a433beb9bb8d1620f75f38d54afdde950aa3b6c6
Browse code

fix vignettes and push upstream

pcastellanoescuder authored on 07/12/2023 19:53:47
Showing 6 changed files
DESCRIPTION
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 Package: POMA
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 Title: Tools for Omics Data Analysis
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-Version: 1.8.53
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+Version: 1.8.54
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 Authors@R:
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     c(person(given = "Pol",
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              family = "Castellano-Escuder",
NEWS.md
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-# POMA 1.8.53
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+# POMA 1.8.54
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 * New POMA theme and colorblind-friendly palette
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 * Available sample normalization (sum and quantile)
README.Rmd
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 | _BioC_ branch 	| Status 	| Version 	| Dependencies 	| Rank 	|
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 |-	|-	|-	|-	|-	|
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 | [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) 	|
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-| [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-1.8.53-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) 	|
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+| [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-1.8.54-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) 	|
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   <!-- badges: end -->
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README.md
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 | *BioC* branch                                                           | Status                                                                                                                                                  | Version                                                                                                                                            | Dependencies                                                                                                                                         | Rank                                                                                                                         |
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 |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
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 | [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) |
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-| [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-1.8.53-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)   |
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+| [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-1.8.54-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)   |
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 <!-- badges: end -->
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vignettes/POMA-normalization.Rmd
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 **Compiled date**: `r Sys.Date()`
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-**Last edited**: 2023-12-06
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+**Last edited**: 2023-12-07
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 **License**: `r packageDescription("POMA")[["License"]]`
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@@ -97,37 +97,37 @@ a <- PomaBoxplots(none,
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 b <- PomaBoxplots(auto_scaling,
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                   x = "samples",
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-                  legend_position = "none") +
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+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Auto Scaling") +
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   ggplot2::theme(axis.text.x = ggplot2::element_blank())
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 c <- PomaBoxplots(level_scaling,
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                   x = "samples",
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-                  legend_position = "none") +
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+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Level Scaling") +
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   ggplot2::theme(axis.text.x = ggplot2::element_blank())
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 d <- PomaBoxplots(log_scaling,
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                   x = "samples",
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-                  legend_position = "none") +
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+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Log Scaling") +
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   ggplot2::theme(axis.text.x = ggplot2::element_blank())
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 e <- PomaBoxplots(log_transformation,
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                   x = "samples",
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-                  legend_position = "none") +
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+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Log Transformation") +
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   ggplot2::theme(axis.text.x = ggplot2::element_blank())
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 f <- PomaBoxplots(vast_scaling,
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                   x = "samples",
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-                  legend_position = "none") +
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+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Vast Scaling") +
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   ggplot2::theme(axis.text.x = ggplot2::element_blank())
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 g <- PomaBoxplots(log_pareto,
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                   x = "samples",
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-                  legend_position = "none") +
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+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Log Pareto") +
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   ggplot2::theme(axis.text.x = ggplot2::element_blank())
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 ```{r, message = FALSE, warning = FALSE}
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 h <- PomaDensity(none,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Not Normalized")
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 i <- PomaDensity(auto_scaling,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Auto Scaling") +
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   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
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                  axis.title.y = ggplot2::element_blank())
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 j <- PomaDensity(level_scaling,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Level Scaling") +
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   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
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                  axis.title.y = ggplot2::element_blank())
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 k <- PomaDensity(log_scaling,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Log Scaling") +
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   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
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                  axis.title.y = ggplot2::element_blank())
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 l <- PomaDensity(log_transformation,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Log Transformation") +
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   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
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                  axis.title.y = ggplot2::element_blank())
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 m <- PomaDensity(vast_scaling,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Vast Scaling") +
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   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
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                  axis.title.y = ggplot2::element_blank())
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 n <- PomaDensity(log_pareto,
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                  x = "features",
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-                 legend_position = "none") +
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+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
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   ggplot2::ggtitle("Log Pareto") +
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   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
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                  axis.title.y = ggplot2::element_blank())
vignettes/POMA-workflow.Rmd
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 **Compiled date**: `r Sys.Date()`
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-**Last edited**: 2023-12-06
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+**Last edited**: 2023-12-07
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 **License**: `r packageDescription("POMA")[["License"]]`
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 library(POMA)
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 ```
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-Additionally, you can load other useful packages for this vignette:
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-
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-```{r, warning = FALSE, message = FALSE}
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-library(ggplot2)
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-library(plotly)
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-```
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-
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 # The POMA Workflow
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 The `POMA` package functions are organized into three sequential, distinct blocks: Data Preparation, Pre-processing, and Statistical Analysis.
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 ```{r, message = FALSE}
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 PomaBoxplots(imputed,
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-             x = "samples",
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-             legend_position = "none") +
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-  ggplot2::ggtitle("Not Normalized") # data before normalization
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+             x = "samples") # data before normalization
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 ```
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 ```{r, message = FALSE}
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 PomaBoxplots(normalized,
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-             x = "samples",
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-             legend_position = "none") +
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-  ggplot2::ggtitle("Normalized") # data after normalization
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+             x = "samples") # data after normalization
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 ```
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 <!-- On the other hand, `PomaDensity` shows the distribution of all features before and after the normalization process.     -->
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 ```{r, message = FALSE}
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 PomaDensity(imputed,
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-            x = "features") +
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-  ggplot2::ggtitle("Not Normalized") # data before normalization
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+            x = "features") # data before normalization
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 ```
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 ```{r, message = FALSE}
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 PomaDensity(normalized,
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-            x = "features") +
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-  ggplot2::ggtitle("Normalized") # data after normalization
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+            x = "features") # data after normalization
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 ```
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 ### Outlier Detection
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 #### T-test
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 ```{r}
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-PomaUnivariate(pre_processed, method = "ttest")
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+pre_processed %>%
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+  PomaUnivariate(method = "ttest")
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 ```
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 <!-- You can also compute a volcano plot using the T-test results.    -->
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 ```{r}
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-PomaVolcano(imputed, pval = "adjusted", labels = TRUE)
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+imputed %>%
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+  PomaVolcano(pval = "adjusted", labels = TRUE)
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 ```
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 #### Wilcoxon Test
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 ```{r, warning = FALSE}
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-PomaUnivariate(pre_processed, method = "mann")
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+pre_processed %>%
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+  PomaUnivariate(method = "mann")
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 ```
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 <!-- ### Limma -->