Regarding visualization of more than 6000 rows using d3heatmap

[pbachali]

I am Prathyusha Bachali, Bioinformatician at Ampel Biosolutions doing microarray data analysis and I used generate heatmaps using heatmap.2 of gplots package. This does not favor me with zooming the data feature in heatmap. But d3heatmap package has this awesome quality where I can zoom the chunks of my heatmap. I am able to generate heatmap using up till 2000 rows. If it is more than that, it is not throwing any error it is generating heatmap but it is leaving blank space but I can see the values if i hover.
I am not sure how to solve this issue. Here is the screenshot of my heatmap.
.
Any help or suggestion would be appreciated.

Thanks,
Prat

[juferban]

Hi Prathyusha,

In case you are still trying to solve this issue I would suggest adding this option to your d3heatmap code:
show_grid = FALSE

I experience this issue in the past where the "cells" are too small due to the amount of data points and the grid lines around each cell (white color lines by default) are creating the illusion of a white canvas.

Hope this helps,

J.

[talgalili]

Hi @pbachali

The heatmaply R package is a new implementation of interactive cluster heatmaps in R which relies on the plotly R package. This is based on a fork of my work in d3heatmap.

The package is availabale from CRAN:
https://cran.r-project.org/package=heatmaply

The feature you've requested is now available by using the new plotly plot_method, for example, using the following code (you can play with larger numbers, and it can still handle them much better than d3heatmap):

library(heatmaply)
bix_x <- matrix(1:10000, 100,100)
heatmaply(bix_x, plot_method = "plotly")