131 lines
1.7 KiB
Plaintext
131 lines
1.7 KiB
Plaintext
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---
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title: "Quick Introduction"
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date: "`r Sys.Date()`"
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author: "Tal Galili"
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output:
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html_vignette:
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toc: yes
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editor_options:
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chunk_output_type: console
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteIndexEntry{A quick introduction to dendextend (start here)}
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-->
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```{r, echo = FALSE, message = FALSE, warning=FALSE}
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library(dendextend)
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library(knitr)
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knitr::opts_chunk$set(
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cache = TRUE,
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dpi = 75,
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fig.width = 6, fig.height = 6,
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# comment = "#>",
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tidy = FALSE)
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# https://stackoverflow.com/questions/24091735/why-pandoc-does-not-retrieve-the-image-file
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# < ! -- rmarkdown v1 -->
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```
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Start
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------------------------------
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Load:
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```{r}
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library(dendextend) #
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```
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Create a dendrogram (if you don't know what `%>%` is, read about it [here](https://CRAN.R-project.org/package=magrittr/vignettes/magrittr.html) ) :
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```{r}
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dend <- c(1:5) %>% dist %>% hclust("ave") %>% as.dendrogram
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```
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Plot:
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```{r}
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plot(dend)
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```
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Get/set labels
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```{r}
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labels(dend)
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labels(dend) <- c("A", "B", "extend", "dend", "C")
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labels(dend)
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```
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Get/set labels' colors
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```{r}
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labels_colors(dend)
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labels_colors(dend) <- rainbow(5)
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labels_colors(dend)
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plot(dend)
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```
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Cut-tree, and color branches
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```{r}
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cutree(dend, k = 2)
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dend <- color_branches(dend, k = 2)
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plot(dend)
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```
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Sort
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```{r}
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dend2 <- sort(dend)
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plot(dend2)
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```
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Compare
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```{r}
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tanglegram( dend, dend2 )
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```
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Cor
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```{r}
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cor_cophenetic( dend, dend2 )
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```
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ggplot2
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```{r}
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library(ggplot2)
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ggplot(dend)
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```
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Send to plot.ly
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```{r}
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# library(plotly)
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# set_credentials_file(...)
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# you'll need to get it from here: https://plot.ly/ggplot2/getting-started/
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# ggplot(dend)
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# py <- plotly()
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# py$ggplotly()
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```
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