ggdendro

Author: chriddyp

_posts/ggplot2/2015-08-03-dendrogram.Rmd

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+---
+title: ggdendro lattice dendrograms | plotly
+name: ggdendro lattice dendrograms
+permalink: ggplot2/ggdendro-dendrograms
+description: How to make a dendrogram with ggdendro and ggplot2
+layout: base
+thumbnail: /images/dendrogram.png
+language: ggplot2
+page_type: example_index
+has_thumbnail: true
+display_as: chart_type
+order: 14
+---
+
+```{r, echo = FALSE, message=FALSE}
+knitr::opts_chunk$set(message = FALSE)
+Sys.setenv("plotly_username"="RPlotBot")
+Sys.setenv("plotly_api_key"="q0lz6r5efr")
+```
+
+
+```{r, message=FALSE, height=900}
+library(ggplot2)
+library(ggdendro)
+library(plotly)
+
+#dendogram data
+x <- as.matrix(scale(mtcars))
+dd.col <- as.dendrogram(hclust(dist(x)))
+dd.row <- as.dendrogram(hclust(dist(t(x))))
+dx <- dendro_data(dd.row)
+dy <- dendro_data(dd.col)
+
+# helper function for creating dendograms
+ggdend <- function(df) {
+  ggplot() +
+    geom_segment(data = df, aes(x=x, y=y, xend=xend, yend=yend)) +
+    labs(x = "", y = "") + theme_minimal() +
+    theme(axis.text = element_blank(), axis.ticks = element_blank(),
+          panel.grid = element_blank())
+}
+
+# x/y dendograms
+px <- ggdend(dx$segments)
+py <- ggdend(dy$segments) + coord_flip()
+
+# heatmap
+col.ord <- order.dendrogram(dd.col)
+row.ord <- order.dendrogram(dd.row)
+xx <- scale(mtcars)[col.ord, row.ord]
+xx_names <- attr(xx, "dimnames")
+df <- as.data.frame(xx)
+colnames(df) <- xx_names[[2]]
+df$car <- xx_names[[1]]
+df$car <- with(df, factor(car, levels=car, ordered=TRUE))
+mdf <- reshape2::melt(df, id.vars="car")
+p <- ggplot(mdf, aes(x = variable, y = car)) + geom_tile(aes(fill = value))
+
+
+# hide axis ticks and grid lines
+eaxis <- list(
+  showticklabels = FALSE,
+  showgrid = FALSE,
+  zeroline = FALSE
+)
+
+p_empty <- plot_ly(filename="r-docs/dendrogram") %>%
+  # note that margin applies to entire plot, so we can
+  # add it here to make tick labels more readable
+  layout(margin = list(l = 200),
+         xaxis = eaxis,
+         yaxis = eaxis)
+
+subplot(px, p_empty, p, py, nrows = 2, margin = 0.01)
+```

_posts/ggplot2/2015-08-03-dendrogram.md

@@ -0,0 +1,74 @@
+---
+title: ggdendro lattice dendrograms | plotly
+name: ggdendro lattice dendrograms
+permalink: ggplot2/ggdendro-dendrograms
+description: How to make a dendrogram with ggdendro and ggplot2
+layout: base
+thumbnail: /images/dendrogram.png
+language: ggplot2
+page_type: example_index
+has_thumbnail: true
+display_as: chart_type
+order: 14
+---
+
+
+
+
+
+```r
+library(ggplot2)
+library(ggdendro)
+library(plotly)
+
+#dendogram data
+x <- as.matrix(scale(mtcars))
+dd.col <- as.dendrogram(hclust(dist(x)))
+dd.row <- as.dendrogram(hclust(dist(t(x))))
+dx <- dendro_data(dd.row)
+dy <- dendro_data(dd.col)
+
+# helper function for creating dendograms
+ggdend <- function(df) {
+  ggplot() +
+    geom_segment(data = df, aes(x=x, y=y, xend=xend, yend=yend)) +
+    labs(x = "", y = "") + theme_minimal() +
+    theme(axis.text = element_blank(), axis.ticks = element_blank(),
+          panel.grid = element_blank())
+}
+
+# x/y dendograms
+px <- ggdend(dx$segments)
+py <- ggdend(dy$segments) + coord_flip()
+
+# heatmap
+col.ord <- order.dendrogram(dd.col)
+row.ord <- order.dendrogram(dd.row)
+xx <- scale(mtcars)[col.ord, row.ord]
+xx_names <- attr(xx, "dimnames")
+df <- as.data.frame(xx)
+colnames(df) <- xx_names[[2]]
+df$car <- xx_names[[1]]
+df$car <- with(df, factor(car, levels=car, ordered=TRUE))
+mdf <- reshape2::melt(df, id.vars="car")
+p <- ggplot(mdf, aes(x = variable, y = car)) + geom_tile(aes(fill = value))
+
+
+# hide axis ticks and grid lines
+eaxis <- list(
+  showticklabels = FALSE,
+  showgrid = FALSE,
+  zeroline = FALSE
+)
+
+p_empty <- plot_ly(filename="r-docs/dendrogram") %>%
+  # note that margin applies to entire plot, so we can
+  # add it here to make tick labels more readable
+  layout(margin = list(l = 200),
+         xaxis = eaxis,
+         yaxis = eaxis)
+
+subplot(px, p_empty, p, py, nrows = 2, margin = 0.01)
+```
+
+<iframe height="900" id="igraph" scrolling="no" seamless="seamless" src="https://plot.ly/~RPlotBot/1166.embed" width="800" frameBorder="0"></iframe>