Error "not numeric" when using crosstalk package with EnhancedVolcano - r

Question

I'd like to implement a cross-talk functionality between a table and plot in both directions:
select the row in the table which will be reflected in the plot
select a dot in the plot which will be reflected in the table. Same idea as here.
I've managed to implement a script, which works beautifully if I make scatter plot with ggplot() and table (both objects cross-talk!). However, when used EnhancedVolcano() and table I got the following error:
Error in EnhancedVolcano(toptable = data_shared, lab = "disp", x = "qsec", :
qsec is not numeric!
If I replace data_shared variable with df_orig, no error is raised, but there is no cross-talking between objects :(
Does this mean that SharedData$new() doesn't recognize numeric values as numeric? How to fix this error?
Any help is highly appreciated.
Thank you
Toy example:
library(plotly) # '4.9.1'
library(DT) # '0.11'
library(crosstalk) # ‘1.0.0’
library(EnhancedVolcano) # ‘1.4.0’
# Input
data1 = mtcars #dim(data1) # 32 11
data_shared = SharedData$new(data1) #, key = c("qsec", "hp"))
# df_orig = data_shared$origData()
# V-Plot
vp =EnhancedVolcano( toptable = data_shared,
lab = 'disp',
x = 'qsec',
y = 'hp',
xlab ='testX',
ylab = 'testY')
bscols(
ggplotly(vp + aes(x= qsec, y= -log10(hp/1000))),
datatable(data_shared, style="bootstrap", class="compact", width="100%",
options=list(deferRender=FALSE, dom='t')))
Same script, which works with ggplot():
data1 = mtcars #dim(data1) # 32 11
data_shared = SharedData$new(data1)
vp = ggplot(data = data_shared, mapping = aes(qsec, hp)) +
geom_point()
bscols(
ggplotly(vp) ,
datatable(data_shared, style="bootstrap", class="compact", width="100%",
options=list(deferRender=FALSE, dom='t')))

Answer 1

Note: Related (same) question was posted at BioStars, and the package author posted an answer, with author's permission copying an answer here:
Hi,
Thanks - that's very useful code and I may add it to the main package vignette, eventually.
I tried it here on my computer and I was able to get it working in my browser, but some components of the original plot seem to have been lost. I think that you just need to convert your column, 'qsec', to numerical values.
Re-using an example from my Vignette, here is a perfectly reproducible example:
library("pasilla")
pasCts <- system.file("extdata", "pasilla_gene_counts.tsv",
package="pasilla", mustWork=TRUE)
pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv",
package="pasilla", mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c("condition","type")]
rownames(coldata) <- sub("fb", "", rownames(coldata))
cts <- cts[, rownames(coldata)]
library("DESeq2")
dds <- DESeqDataSetFromMatrix(countData = cts,
colData = coldata,
design = ~ condition)
featureData <- data.frame(gene=rownames(cts))
mcols(dds) <- DataFrame(mcols(dds), featureData)
dds <- DESeq(dds)
res <- results(dds)
library(EnhancedVolcano)
p1 <- EnhancedVolcano(res,
lab = rownames(res),
x = "log2FoldChange",
y = "pvalue",
pCutoff = 10e-4,
FCcutoff = 2,
xlim = c(-5.5, 5.5),
ylim = c(0, -log10(10e-12)),
pointSize = c(ifelse(res$log2FoldChange>2, 8, 1)),
labSize = 4.0,
shape = c(6, 6, 19, 16),
title = "DESeq2 results",
subtitle = "Differential expression",
caption = "FC cutoff, 1.333; p-value cutoff, 10e-4",
legendPosition = "right",
legendLabSize = 14,
col = c("grey30", "forestgreen", "royalblue", "red2"),
colAlpha = 0.9,
drawConnectors = TRUE,
hline = c(10e-8),
widthConnectors = 0.5)
p1 <- p1 +
ggplot2::coord_cartesian(xlim=c(-6, 6)) +
ggplot2::scale_x_continuous(
breaks=seq(-6,6, 1))
library(plotly)
library(DT)
library(crosstalk)
bscols(
ggplotly(p1 + aes(x= log2FoldChange, y= -log10(pvalue))),
datatable(
data.frame(res),
style="bootstrap",
class="compact", width="100%",
options=list(deferRender=FALSE, dom='t')))
Unfortunately, plotly and/or bscols don't like the use of bquote(), so, one cannot have the fancy axes names that I use in EnhancedVolcano:
... + xlab(bquote(~Log[2] ~ "fold change")) + ylab(bquote(~-Log[10] ~ italic(P)))
When i try to add these, it throws an error.
Kevin

Answer 2

tried to modify few things in volcano function, got following error:
Error in as.data.frame.default(toptable) :
cannot coerce class ‘c("SharedData", "R6")’ to a data.frame
not sure yet, how to fix it.