diff --git a/README.Rmd b/README.Rmd
index 56985fc5..97315602 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -6,7 +6,7 @@ bibliography: paper/bibliography.bib
-[](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
+[](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
[](code_of_conduct.md)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://www.codefactor.io/repository/github/adrientaudiere/miscmetabar/overview/master)
@@ -26,7 +26,7 @@ knitr::opts_chunk$set(
)
```
-# MiscMetabar 
+# MiscMetabar 
See the pkgdown documentation site [here](https://adrientaudiere.github.io/MiscMetabar/) and the [package paper](https://doi.org/10.21105/joss.06038) in the Journal Of Open Softwares.
@@ -46,7 +46,7 @@ BiocManager.
You can install the stable version from [GitHub](https://github.com/)
with:
-```{r, results = 'hide'}
+```{r, results = 'hide', eval=FALSE}
if (!require("devtools", quietly = TRUE)) {
install.packages("devtools")
}
@@ -56,7 +56,7 @@ devtools::install_github("adrientaudiere/MiscMetabar")
You can install the development version from
[GitHub](https://github.com/) with:
-```{r, results = 'hide'}
+```{r, results = 'hide', eval=FALSE}
if (!require("devtools", quietly = TRUE)) {
install.packages("devtools")
}
@@ -71,7 +71,7 @@ See vignettes in the [MiscMetabar](https://adrientaudiere.github.io/MiscMetabar/
For an introduction to metabarcoding in R, Please visite the [state of the field](https://adrientaudiere.github.io/MiscMetabar/articles/states_of_fields_in_R.html) vignettes. The [import, export and track](https://adrientaudiere.github.io/MiscMetabar/articles/import_export_track.html) vignette explains how import and export `phyloseq` object. Its also show how to summarize useful information (number of sequences, samples and clusters) accross bioinformatic pipelines.
If you are interested in ecological metrics, see the vignettes describing [alpha-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/alpha-div.html) and [beta-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/beta-div.html) analysis.
-The vignette [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data-filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
+The vignette [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data-filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler](https://adrientaudiere.github.io/MiscMetabar/articles/tengeler.html) explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
For developers, I also wrote a vignette describing som [rules of codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html).
diff --git a/README.md b/README.md
index 4e3b2f63..53904e21 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
-[](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
+[](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
[](code_of_conduct.md)
[](https://www.gnu.org
-# MiscMetabar
+# MiscMetabar
See the pkgdown documentation site
[here](https://adrientaudiere.github.io/MiscMetabar/) and the [package
@@ -91,8 +91,10 @@ samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html)
describes some data-filtering processes using MiscMetabar and the
[reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html)
tutorial introduces the different way of clustering already-clustered
-OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et
-al. (2020) using some MiscMetabar functions.
+OTU/ASV. The vignette
+[tengeler](https://adrientaudiere.github.io/MiscMetabar/articles/tengeler.html)
+explore the dataset from Tengeler et al. (2020) using some MiscMetabar
+functions.
For developers, I also wrote a vignette describing som [rules of
codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html).
diff --git a/man/ggvenn_pq.Rd b/man/ggvenn_pq.Rd
index 927ad0ed..0cfa9a64 100644
--- a/man/ggvenn_pq.Rd
+++ b/man/ggvenn_pq.Rd
@@ -62,6 +62,8 @@ of plots.
Note that you can use ggplot2 function to customize the plot
for ex. \code{+ scale_fill_distiller(palette = "BuPu", direction = 1)}
+and \code{+ scale_x_continuous(expand = expansion(mult = 0.5))}. See
+examples.
}
\examples{
data(data_fungi)
@@ -80,9 +82,10 @@ data_fungi2 <- subset_samples(data_fungi, data_fungi@sam_data$Tree_name == "A10-
data_fungi@sam_data$Height \%in\% c("Low", "High"))
ggvenn_pq(data_fungi2, fact = "Height")
-ggvenn_pq(data_fungi, fact = "Height", add_nb_sequences = TRUE, set_size = 4)
+ggvenn_pq(data_fungi, fact = "Height", add_nb_sequences = TRUE, set_size = 4)
ggvenn_pq(data_fungi, fact = "Height", rarefy_before_merging = TRUE)
-ggvenn_pq(data_fungi, fact = "Height", rarefy_after_merging = TRUE)
+ggvenn_pq(data_fungi, fact = "Height", rarefy_after_merging = TRUE) +
+ scale_x_continuous(expand = expansion(mult = 0.5))
}
\seealso{
diff --git a/man/multitax_bar_pq.Rd b/man/multitax_bar_pq.Rd
index b2b62b0c..8d7627b9 100644
--- a/man/multitax_bar_pq.Rd
+++ b/man/multitax_bar_pq.Rd
@@ -2,7 +2,8 @@
% Please edit documentation in R/plot_functions.R
\name{multitax_bar_pq}
\alias{multitax_bar_pq}
-\title{Plot taxonomic distribution across 3 levels}
+\title{Plot taxonomic distribution across 3 taxonomic levels and optionally
+one sample factor}
\usage{
multitax_bar_pq(
physeq,
@@ -42,7 +43,7 @@ A ggplot2 graphic
\description{
\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
-Note that lvl3need to be nested in lvl2 which need to be nested
+Note that lvl3 need to be nested in lvl2 which need to be nested
in lvl1
}
\examples{