save as vector graphic

[DoaneAS]

Hi,

Thanks for this package it's very useful.

Wondering is it possible to save as a vector graphic?

Here's a heatmap of some analysis, saved as pdf.
motifsGainedExpressed.inpeaks.eta0.1.pdf

It seems the matrix is encoded as a raster image. Maybe something I am doing with the pdf device in R?

Thanks!

Ashley

[AliciaSchep]

Hi Ashley,

When saving a static version, it renders the heatmap and then takes a snapshot, which is why it would be a raster image even if saving as a pdf.

I think it would be nicer if the heatmaps could be saved as vector graphics. I had looked into whether that would be possible sometime in the past, and remember that it seemed like it would be difficult. I might revisit this sometime in the future, but likely not anytime soon.

[DoaneAS]

Ok, thank you Alicia. Great package!

[fboehm]

Hi, Is it possible to save heatmaps with plotly::orca()? I have been unable to succeed in this task.

mtcars %>% as.matrix() %>% main_heatmap() %>% plotly::orca(file = "foo.svg")

The above R code returns an error: Error in UseMethod("plotly_build") : no applicable method for 'plotly_build' applied to an object of class "c('IheatmapHorizontal', 'Iheatmap')"

Do you have suggestions on what I might do to make the heatmap usable by plotly::orca? I'm afraid that I don't yet know enough about the methods that you use in iheatmapr. Thank you.

[mschilli87]

@fboehm: I have no time to check right now but I think there is an as.plotly function (or the like) that should do what you need.

[fboehm]

Thanks, @mschilli87! Do you know which package contains the as.plotly function? It looks like it is not exported from iheatmapr or plotly.

Thanks!

[mschilli87]

@fboehm: Looks like it was called as_plotly but was removed in 3e09ad680d848f380681c63f8d317e0eb4859338. Not sure if to_widget can be exploited to use orca but probably not. You might be able to look at plotly's (the R package) implementation of the orca (R) function though to come up with a way to pass the iheatmapr object to an external orca (binary) call. Sorry that I can't be of more help as of now.

[fboehm]

Thank you, @mschilli87! I will check out the R code for the function plotly::orca. Thanks again!

[mschilli87]

@fboehm: OK - I gave this a couple of minutes and the best I came up with is this:

library(magrittr)
library(iheatmapr)
library(plotly)

hm <-
  mtcars %>%
  as.matrix %>%
  main_heatmap

pl <- iheatmapr:::to_plotly_list(hm)

pl %>%
  orca(file = "foo.svg")

This at least renders the heatmap and legend in the SVG but as to_plotly_list is internal (hence the three :) this expectedly doesn't go all the way. But I hope it helps to figure out the rest and maybe @AliciaSchep has some additional pointers for you.

[fboehm]

Thank you @mschilli87! I'll use your code and see if I can extend it. Thanks again!!

[AliciaSchep]

Thanks @mschilli87 for your solution! It seems like it might make sense to export (and probably rename) the to_plotly_list function to ease this use case.

[AliciaSchep]

An update on this issue -- latest 'dev' version of the package (0.4.10, master branch) exports the to_plotly_list function as well as a companion to_plotly_json which additionally converts to JSON.