](https://colab.research.google.com/github/fernandoroa/IFjupyter/blob/main/",
note,
"){target='_blank'}
[Github](https://github.com/fernandoroa/IFjupyter/blob/main/",
note,
"){target='_blank'}
|
[](https://colab.research.google.com/github/fernandoroa/IFjupyter/blob/main/",
note,
"){target='_blank'}
|
[Github](https://github.com/fernandoroa/IFjupyter/blob/main/",
note,
"){target='_blank'}
|
[Raw](https://github.com/fernandoroa/IFjupyter/raw/main/", note, "){target='_blank'} |
")
```
[Mariana PC Telles](http://lattes.cnpq.br/4648436798023532)
```{r include=FALSE,eval=FALSE}
# automatically create a bib database for R packages, this is currently not used by vignette refs/packages2.bib
knitr::write_bib(c(
.packages(), "bookdown", "knitr", "rmarkdown", "devtools", "pkgdown", "crayon", "ggtree", "ggplot2", "ggpubr", "phytools", "plyr", "dplyr", "tidyr", "rentrez"
), "refs/packages2.bib")
```
```{r, echo=F}
chapterFile_jupyter <- "../parts/01-jupyter.Rmd"
if (file.exists(chapterFile_jupyter)) {
childExists_jupyter <- TRUE
child_docs_jupyter <- chapterFile_jupyter
} else {
childExists_jupyter <- FALSE
child_docs_jupyter <- ""
}
```
```{r, child = child_docs_jupyter, eval=childExists_jupyter}
```
```{r, echo=F}
chapterFile_first <- "../parts/02-first.Rmd"
if (file.exists(chapterFile_first)) {
childExists_first <- TRUE
child_docs_first <- chapterFile_first
} else {
childExists_first <- FALSE
child_docs_first <- ""
}
```
```{r, child = child_docs_first, eval=childExists_first}
```
```{r, echo=F}
chapterFile_minimal <- "../chaptersBLOCK/03-minimal.Rmd"
if (file.exists(chapterFile_minimal)) {
childExists_minimal <- TRUE
child_docs_minimal <- chapterFile_minimal
} else {
childExists_minimal <- FALSE
child_docs_minimal <- ""
}
```
```{r, child = child_docs_minimal, eval=childExists_minimal}
```
```{r, results="asis", eval=!childExists_minimal, echo=FALSE}
cat("# Minimal Examples")
```
```{r, results="asis", eval=!childExists_minimal, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#minimal-examples)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_minimal, comment=NA}
note <- "03-minimal.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile_plotting <- "../chaptersBLOCK/04-plotting.Rmd"
if (file.exists(chapterFile_plotting)) {
childExists_plotting <- TRUE
child_docs_plotting <- chapterFile_plotting
} else {
childExists_plotting <- FALSE
child_docs_plotting <- ""
}
```
```{r, child = child_docs_plotting, eval=childExists_plotting}
```
```{r, results="asis", eval=!childExists_plotting, echo=FALSE}
cat("# Plotting chromosomes")
```
```{r, results="asis", eval=!childExists_plotting, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#plotting-chromosomes)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_plotting, comment=NA}
note <- "04-plotting.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile_multiple <- "../chaptersBLOCK/05-multiple.Rmd"
if (file.exists(chapterFile_multiple)) {
childExists_multiple <- TRUE
child_docs_multiple <- chapterFile_multiple
} else {
childExists_multiple <- FALSE
child_docs_multiple <- ""
}
```
```{r, child = child_docs_multiple, eval=childExists_multiple}
```
```{r, results="asis", eval=!childExists_multiple, echo=FALSE}
cat("# Several OTUs")
```
```{r, results="asis", eval=!childExists_multiple, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#multiple-otus)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_multiple, comment=NA}
note <- "05-multiple.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile_units <- "../chaptersBLOCK/06-units.Rmd"
if (file.exists(chapterFile_units)) {
childExists_units <- TRUE
child_docs_units <- chapterFile_units
} else {
childExists_units <- FALSE
child_docs_units <- ""
}
```
```{r, child = child_docs_units, eval=childExists_units}
```
```{r, results="asis", eval=!childExists_units, echo=FALSE}
cat("# Changing Units")
```
```{r, results="asis", eval=!childExists_units, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#changing-units)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_units, comment=NA}
note <- "06-units.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile0 <- "../chaptersBLOCK/07-gish.Rmd"
if (file.exists(chapterFile0)) {
childExists0 <- TRUE
child_docs0 <- chapterFile0
} else {
childExists0 <- FALSE
child_docs0 <- ""
}
```
```{r, child = child_docs0, eval=childExists0}
```
```{r, results="asis", eval=!childExists0, echo=FALSE}
cat("# GISH")
```
```{r, results="asis", eval=!childExists0, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#gish)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists0, comment=NA}
note <- "07-gish.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile1 <- "../chaptersBLOCK/08-groups.Rmd"
if (file.exists(chapterFile1)) {
childExists1 <- TRUE
child_docs1 <- chapterFile1
} else {
childExists1 <- FALSE
child_docs1 <- ""
}
```
```{r, child = child_docs1, eval=childExists1}
```
```{r, results="asis", eval=!childExists1, echo=FALSE}
cat("# Using groups")
```
```{r, results="asis", eval=!childExists1, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#groups)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists1, comment=NA}
note <- "08-groups.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile2 <- "../chaptersBLOCK/09-circular.Rmd"
if (file.exists(chapterFile2)) {
childExists2 <- TRUE
child_docs2 <- chapterFile2
} else {
childExists2 <- FALSE
child_docs2 <- ""
}
```
```{r, child = child_docs2, eval = childExists2}
```
```{r, results="asis", eval=!childExists2, echo=FALSE}
cat("# Circular plots")
```
```{r, results="asis", eval=!childExists2, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#circular-plots)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists2, comment=NA}
note <- "09-circular.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile3 <- "../chaptersBLOCK/10-phylogeny.Rmd"
if (file.exists(chapterFile3)) {
childExists3 <- TRUE
child_docs3 <- chapterFile3
} else {
childExists3 <- FALSE
child_docs3 <- ""
}
```
```{r, child = child_docs3, eval=childExists3}
```
```{r, results="asis", eval=!childExists3, echo=FALSE}
cat("# Plotting alongside phylogeny")
```
```{r, results="asis", eval=!childExists3, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#plotting-alongside-phylogeny)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists3, comment=NA}
note <- "10-phylogeny.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile <- "../chaptersBLOCK/11-citrushelp.Rmd"
if (file.exists(chapterFile)) {
childExists <- TRUE
child_docs <- chapterFile
} else {
childExists <- FALSE
child_docs <- ""
}
```
```{r, child = child_docs, eval=childExists}
```
```{r, results="asis", eval=!childExists, echo=FALSE}
cat("# *Citrus*")
```
```{r, results="asis", eval=!childExists, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#citrus)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists, comment=NA}
note <- "11-citrushelp.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile4 <- "../chaptersBLOCK/12-human.Rmd"
if (file.exists(chapterFile4)) {
childExists4 <- TRUE
child_docs4 <- chapterFile4
} else {
childExists4 <- FALSE
child_docs4 <- ""
}
```
```{r, child = child_docs4, eval=childExists4}
```
```{r, results="asis", eval=!childExists4, echo=FALSE}
cat("# Human karyotype")
```
```{r, results="asis", eval=!childExists4, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#human-karyotype)")
```
```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists4, comment=NA}
note <- "12-human.ipynb"
pasteLinks(note)
```
```{r, echo=F}
chapterFile_param <- "../chaptersBLOCK/13-functions.Rmd"
if (file.exists(chapterFile_param)) {
childExists_param <- TRUE
child_docs_param <- chapterFile_param
} else {
childExists_param <- FALSE
child_docs_param <- ""
}
```
```{r, child = child_docs_param, eval=childExists_param}
```
```{r, results="asis", eval=!childExists_param, echo=FALSE}
cat("# Functions")
```
```{r, results="asis", eval=!childExists_param, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#functions)")
```
```{r, echo=F}
chapterFile_data <- "../chaptersBLOCK/14-datasets.Rmd"
if (file.exists(chapterFile_data)) {
childExists_data <- TRUE
child_docs_data <- chapterFile_data
} else {
childExists_data <- FALSE
child_docs_data <- ""
}
```
```{r, child = child_docs_data, eval=childExists_data}
```
```{r, results="asis", eval=!childExists_data, echo=FALSE}
cat("# Datasets")
```
```{r, results="asis", eval=!childExists_data, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#datasets)")
```
```{r, echo=F}
chapterFile_news <- "../chaptersBLOCK/15-news.Rmd"
if (file.exists(chapterFile_news)) {
childExists_news <- TRUE
child_docs_news <- chapterFile_news
} else {
childExists_news <- FALSE
child_docs_news <- ""
}
```
```{r, child = child_docs_news, eval=childExists_news}
```
```{r, results="asis", eval=!childExists_news, echo=FALSE}
cat("# News {-}")
```
```{r, results="asis", eval=!childExists_news, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#news)")
```
# References {-}
::: {#refs_normal}
:::
## R-packages {-}
::: {#refs_software}
:::
## Shiny App {-}
::: {#refs_shiny}
:::
## Documentation {-}
::: {#refs_docs}
:::