Corresponding shinyHeatmaply functions for d3heatmap?

[evanbiederstedt]

Hi @yonicd

Thanks for the excellent work!

This might be an unreasonable question, but perhaps it could be useful for other users in a similar situation:

The package d3heatmap is no longer on CRAN and no longer maintained, as described in the README on github: https://github.com/rstudio/d3heatmap

d3heatmap is not actively maintained. You might consider using a newer heatmap package like heatmaply.

So, I would like to port my current code to the something equivalent. Currently I use d3heatmap in a shiny application, with the following calls:

d3heatmap::renderD3heatmap() and d3heatmap::d3heatmapOutput().

Are there equivalents in shinyHeatmaply for users looking to (easily) port their code? Does the same functionality exist with shinyHeatmaply? (Is this obvious?)

Best, Evan

[yonicd]

Great question. @talgalili author of {heatmaply} would be a better person to ask about casting objects into heatmaply.

[evanbiederstedt]

Thanks. Including you both @yonicd @talgalili as there are some questions about how this interacts with shiny.

I think the best result for this discussion would be some explanation for d3heatmap users who to port their code, though if not currently possible, perhaps this requires some coding (with which I'm happy to help out)

[talgalili]

Hey, just to check, why would you prefer to use d3heatmap over heatmaply?

On Thu, Oct 1, 2020 at 2:08 PM evanbiederstedt notifications@github.com wrote:

Thanks. Including you both @yonicd https://github.com/yonicd @talgalili https://github.com/talgalili as there are some questions about how this interacts with shiny.

I think the best result for this discussion would be some explanation for d3heatmap users who to port their code, though if not currently possible, perhaps this requires some coding (with which I'm happy to help out)

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[evanbiederstedt]

Hi @talgalili

Thanks for the great package.

why would you prefer to use d3heatmap over heatmaply?

I don't---I think there's some confusion based on my explanation above:

• I already have legacy code with d3heatmap. Given d3heatmap is now defunct, I would like to replace it with e.g. heatmaply.
• My problem is, I am using d3heatmap in a shiny app using d3heatmap::renderD3heatmap() and d3heatmap::d3heatmapOutput().

So my question is, how can I remove these functions and replace them with heatmaply and shinyHeatmaply?

Make sense?

Thanks, Evan

[talgalili]

No clue. Maybe Alan would know. I'll cc him.

On Thu, Oct 1, 2020, 18:43 evanbiederstedt notifications@github.com wrote:

Hi @talgalili https://github.com/talgalili

Thanks for the great package.

why would you prefer to use d3heatmap over heatmaply?

I don't---I think there's some confusion based on my explanation above:

• I already have legacy code with d3heatmap. Given d3heatmap is now defunct, I would like to replace it with e.g. heatmaply.
• My problem is, I am using d3heatmap in a shiny app using d3heatmap::renderD3heatmap() and d3heatmap::d3heatmapOutput().

So my question is, how can I remove these functions and replace them with heatmaply and shinyHeatmaply?

Make sense?

Thanks, Evan

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[evanbiederstedt]

The best outcome for the R community would be some instructions in the associated READMEs for users trying to update their code.

Perhaps we need to do some development too; I'm not sure what the current state of affairs is in terms of replacing d3heatmap

[alanocallaghan]

Most of the arguments should have a pretty clear correspondence. I don't have the time to write documentation on porting between the two

It's been several years since I looked at the d3heatmap source; I think all of the functionality in d3heatmap and more is replicated in heatmaply.

[evanbiederstedt]

Thanks for the response @Alanocallaghan

Most of the arguments should have a pretty clear correspondence.

This is true. However, I think the fundamental confusion is that I'm not sure how d3heatmap::renderD3heatmap() and d3heatmap::d3heatmapOutput() would work with heatmaply or shinyHeatmaply.

Are there equivalent functions?

[alanocallaghan]

I never used those 2 functions in d3heatmap. From a cursory google it seems you want plotlyOutput and renderPlotly from plotly

[evanbiederstedt]

That works perfectly; I never considered that, as I've been used to using those functions differently.

• d3heatmap() corresponds to heatmaply()
• For d3heatmap::d3heatmapOutput(), use plotly::plotlyOutput()
• For d3heatmap::d3heatmapOutput(), use plotly::renderPlotly()

I haven't noticed any porting issues, but perhaps there are some I missed.

I sincerely appreciate the help! Thank you, Evan

[talgalili]

Glad you got an answer @evanbiederstedt . Do you have a link to your project, so we might learn of your use case? (if not that's also fine, but wanted to invite you to share, in case you have something public)

[evanbiederstedt]

Sure, here you go: https://github.com/kharchenkolab/conosViz

I appreciate your help, everyone! And thank you for the great software! If you're interested, I think a quick note in the README somewhere will help many users porting legacy code. I'm happy to make a PR

Thanks, Evan

[talgalili]

Sure, please make a PR (here or in heatnaply) and I'll take a look.

Cheers T

On Thu, Oct 1, 2020, 23:06 evanbiederstedt notifications@github.com wrote:

Sure, here you go: https://github.com/kharchenkolab/conosViz

I appreciate your help, everyone! And thank you for the great software! If you're interested, I think a quick note in the README somewhere will help many users porting legacy code. I'm happy to make a PR

Thanks, Evan

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[evanbiederstedt]

FWIW, it does look there are some differences in how the dendrograms are rendered in Rowv and Colv, but I haven't investigated this deeply.