Controlling the shared legend when adding a ggplot dendrogram plot to a plotly heatmap

by dan   Last Updated January 14, 2018 12:26 PM

I have genes x samples expression data I'd like to generate a plotly heatmap for and add the samples dendrogram ggplot to.

Here are my data:

set.seed(1)
mat <- matrix(rnorm(100*10),100,10,dimnames = list(paste0("G",1:100),paste0("S",1:10)))

Here's the clustering and dendrograms:

library(dendsort)
library(dplyr)

col.hc <- hclust(dist(t(mat))) %>% dendsort::dendsort(.)
col.dend <- as.dendrogram(col.hc)
col.ord <- order.dendrogram(col.dend)
row.hc <- hclust(dist(mat)) %>% dendsort::dendsort(.)
row.dend <- as.dendrogram(row.hc)
row.ord <- order.dendrogram(row.dend)
mat <- mat[row.ord,col.ord]

Here I'm creating a ggplot from col.dend, using dendextend. Note that all legend associated text and ticks are suppressed:

library(dendextend)
library(ggplot2)

col.gg.dend <- dendextend::as.ggdend(col.dend)
col.gg.dend.ggplot <- ggplot(col.gg.dend,labels=F)+guides(fill=F)+theme_minimal()+
  theme(axis.title=element_blank(),axis.text=element_blank(),axis.ticks=element_blank(),panel.grid=element_blank(),legend.position="none",legend.text=element_blank(),legend.background=element_blank(),legend.key=element_blank())

And here I'm creating the plotly heatmap and adding col.gg.dend.ggplot using plotly::subplot:

library(plotly)
library(reshape2)
library(grDevices)

plot.df <- reshape2::melt(mat,varnames=c("gene","sample"),value.name="value")

heatmap.plot <- plot_ly(z=c(plot.df$value),x=plot.df$sample,y=plot.df$gene,colors=colorRamp(c("darkblue","white","darkred")),type="heatmap",colorbar=list(title="Expression",len=0.4)) %>%
  layout(yaxis=list(title="Gene"),xaxis=list(title="Sample"))

empty.axis <- list(showticklabels=F,showgrid=F,zeroline=F,title=NULL)
empty.plot <- plot_ly() %>% layout(margin=list(l=200),xaxis=empty.axis,yaxis=empty.axis)
subplot(plotly_build(col.gg.dend.ggplot),empty.plot,heatmap.plot,nrows=2,margin=c(0,0,0,0),heights=c(0.2,0.8),widths=c(0.8,0.2))

which gives me: enter image description here

All of this works nicely except for having the bottom part added to the heatmap legend (black,solid,1) and (NA,1), which I'd like to remove/suppress.

Note that plotly_build(col.gg.dend.ggplot) draws the dendrogram without that legend part.



Answers 1


A relatively simple workaround is to do:

subplot(col.gg.dend.ggplot,
        plotly_empty(), 
        heatmap.plot,
        nrows = 2,
        margin = c(0,0,0,0),
        heights = c(0.2,0.8),
        widths = c(0.8,0.2)) %>%
  layout(showlegend = FALSE)

enter image description here

Why it was there in the first place I can not say exactly but I trust it is related to this SO question. Even thought colorbar is not the same as a legend.

layout options found later in the sequence of plots will override options found earlier in the sequence.

Since if you just reverse the order of the subplots.

subplot(heatmap.plot,
        plotly_empty(), 
        col.gg.dend.ggplot,
        nrows = 2,
        margin = c(0,0,0,0),
        heights = c(0.2,0.8),
        widths = c(0.8,0.2))

enter image description here

the artifact is gone.

Do note that within subplot you need not call ggplotly or plotly_build on ggplot objects. And an empty plot can be called by plotly_empty().

Another way to avoid the issue is to use ggdendro:

library(ggdendro)
d.col <- dendro_data(col.dend)

col.2 <- ggplot() +
  geom_segment(data = d.col$segments, 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())

subplot(col.2,
        plotly_empty(), 
        heatmap.plot,
        nrows = 2,
        margin = c(0,0,0,0),
        heights = c(0.2,0.8),
        widths = c(0.8,0.2)) 

yielding the same plot as the first one posted.

missuse
missuse
January 14, 2018 12:10 PM

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