Managing a common legend when adding a ggplot dendrogram graphic to a graphic template

Question

I have genesx expression data samplesI would like to generate a plotly heatmapfor and add samples dendrogram ggplotto.

Here are my details:

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

Here clusteringand 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 create ggplotfrom col.dend, using dendextend. Please note that all legendrelated textand tickssuppressed:

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 create plotly heatmapand add col.gg.dend.ggplotwith 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:

All this works great, except that the bottom is added to heatmap legend (black,solid,1)and (NA,1)which I would like to remove / disable.

Please note that plotly_build(col.gg.dend.ggplot)draws dendrogramwithout this part legend.

Answer 1

:

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)

fooobar.com/questions/1692152/....

, , , .

.

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))

.

, , :

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

, , , , .

, subplot ggplotly plotly_build ggplot. plotly_empty().

- 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)) 

, .

Answer 2

Heatmaply ( , ):

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

heatmaply(mat, dendrogram="column", col = cool_warm, key.title = "Expression", plot_method = "plotly")

, plot_method="plotly.