fix vignettes and push upstream

pcastellanoescuder · Dec 7, 2023 · a433beb · a433beb
1 parent c93cd47
commit a433beb
Show file tree

Hide file tree

Showing 6 changed files with 29 additions and 39 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: POMA
 Title: Tools for Omics Data Analysis   
-Version: 1.8.53
+Version: 1.8.54
 Authors@R: 
     c(person(given = "Pol",
              family = "Castellano-Escuder",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# POMA 1.8.53
+# POMA 1.8.54
 
 * New POMA theme and colorblind-friendly palette
 * Available sample normalization (sum and quantile)

diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,7 @@ 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-1.8.53-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) 	|
+| [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) 	|
 
   <!-- badges: end -->
 

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-1.8.53-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)   |
+| [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)   |
 
 <!-- badges: end -->
 

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**: 2023-12-06
+**Last edited**: 2023-12-07
 
 **License**: `r packageDescription("POMA")[["License"]]`
 
@@ -97,37 +97,37 @@ a <- PomaBoxplots(none,
 
 b <- PomaBoxplots(auto_scaling, 
                   x = "samples", 
-                  legend_position = "none") +
+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Auto Scaling") +
   ggplot2::theme(axis.text.x = ggplot2::element_blank())
 
 c <- PomaBoxplots(level_scaling, 
                   x = "samples", 
-                  legend_position = "none") +
+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Level Scaling") +
   ggplot2::theme(axis.text.x = ggplot2::element_blank())
 
 d <- PomaBoxplots(log_scaling, 
                   x = "samples", 
-                  legend_position = "none") +
+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Log Scaling") +
   ggplot2::theme(axis.text.x = ggplot2::element_blank())
 
 e <- PomaBoxplots(log_transformation, 
                   x = "samples", 
-                  legend_position = "none") +
+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Log Transformation") +
   ggplot2::theme(axis.text.x = ggplot2::element_blank())
 
 f <- PomaBoxplots(vast_scaling, 
                   x = "samples", 
-                  legend_position = "none") +
+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Vast Scaling") +
   ggplot2::theme(axis.text.x = ggplot2::element_blank())
 
 g <- PomaBoxplots(log_pareto, 
                   x = "samples", 
-                  legend_position = "none") +
+                  theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Log Pareto") +
   ggplot2::theme(axis.text.x = ggplot2::element_blank())
 
@@ -142,47 +142,47 @@ Here we can evaluate the normalization effects on features.
 ```{r, message = FALSE, warning = FALSE}
 h <- PomaDensity(none, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Not Normalized")
 
 i <- PomaDensity(auto_scaling, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Auto Scaling") +
   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
                  axis.title.y = ggplot2::element_blank())
 
 j <- PomaDensity(level_scaling, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Level Scaling") +
   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
                  axis.title.y = ggplot2::element_blank())
 
 k <- PomaDensity(log_scaling, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Log Scaling") +
   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
                  axis.title.y = ggplot2::element_blank())
 
 l <- PomaDensity(log_transformation, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Log Transformation") +
   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
                  axis.title.y = ggplot2::element_blank())
 
 m <- PomaDensity(vast_scaling, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Vast Scaling") +
   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
                  axis.title.y = ggplot2::element_blank())
 
 n <- PomaDensity(log_pareto, 
                  x = "features", 
-                 legend_position = "none") +
+                 theme_params = list(legend_title = FALSE, legend_position = "none")) +
   ggplot2::ggtitle("Log Pareto") +
   ggplot2::theme(axis.title.x = ggplot2::element_blank(),
                  axis.title.y = ggplot2::element_blank())

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**: 2023-12-06
+**Last edited**: 2023-12-07
 
 **License**: `r packageDescription("POMA")[["License"]]`
 
@@ -46,13 +46,6 @@ BiocManager::install("POMA")
 library(POMA)
 ```
 
-Additionally, you can load other useful packages for this vignette:
-
-```{r, warning = FALSE, message = FALSE}
-library(ggplot2)
-library(plotly)
-```
-
 # The POMA Workflow
 
 The `POMA` package functions are organized into three sequential, distinct blocks: Data Preparation, Pre-processing, and Statistical Analysis.
@@ -122,30 +115,24 @@ normalized
 
 ```{r, message = FALSE}
 PomaBoxplots(imputed, 
-             x = "samples",
-             legend_position = "none") +
-  ggplot2::ggtitle("Not Normalized") # data before normalization
+             x = "samples") # data before normalization
 ```
 
 ```{r, message = FALSE}
 PomaBoxplots(normalized, 
-             x = "samples", 
-             legend_position = "none") +
-  ggplot2::ggtitle("Normalized") # data after normalization
+             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") +
-  ggplot2::ggtitle("Not Normalized") # data before normalization
+            x = "features") # data before normalization
 ```
 
 ```{r, message = FALSE}
 PomaDensity(normalized, 
-            x = "features") +
-  ggplot2::ggtitle("Normalized") # data after normalization
+            x = "features") # data after normalization
 ```
 
 ### Outlier Detection
@@ -171,19 +158,22 @@ pre_processed
 #### T-test
 
 ```{r}
-PomaUnivariate(pre_processed, method = "ttest")
+pre_processed %>% 
+  PomaUnivariate(method = "ttest")
 ```
 
 <!-- You can also compute a volcano plot using the T-test results.    -->
 
 ```{r}
-PomaVolcano(imputed, pval = "adjusted", labels = TRUE)
+imputed %>% 
+  PomaVolcano(pval = "adjusted", labels = TRUE)
 ```
 
 #### Wilcoxon Test
 
 ```{r, warning = FALSE}
-PomaUnivariate(pre_processed, method = "mann")
+pre_processed %>% 
+  PomaUnivariate(method = "mann")
 ```
 
 <!-- ### Limma -->