A problem while using MetaboAnalystR to generate Heatmap

Hi, guys

I am trying to run MetaboAnalystR to save my time for the data processing. It works very well for plots like Volcano plot, PLSDA 2D score, and random forest. However, I tried to follow the tutorial to use “PlotHeatMap” to generate the heatmap, it only generates a “heatmap_0_.json” file instead of the png of pdf files by default. Is there anyone could help me out, please?


I am experiencing the exact same issue. I’ve been trying to find a solution with no success so far.

It seems that very few people use R to save time, don’t know why only the heatmap has the issue.

Hi all,

The Heatmap is readily available for download from our website. As shown below, you can click the SVG and PNG button to download the figure generated online. Or you can click the paint icon to generate a local static version which might be slightly different with the interactive heatmap. A png file will be created in the download page once you click the submit button in the Graphic Center dialogue.

Hope this helps!

Hi, Yao

Many thanks for your reply. Yes, the website works very well to generate good figures. But I have to use MetaboAnalystR in “R” because I have too much data to process sometimes. It saves us a lot of time to run code to do the batch process.

So far Every figure can be generated by the R code like the volcano plot, and PLSDA plots, just except the heatmap. I am still using the R code because it still helps me much more time than working on the website to generate figures one by one, though I still need to use the website one time to have the heatmap. So I tried my luck to ask everyone for suggestions.


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