Thursday 2 June 2016

GOPlot package for visualizing functional omics data

I recently stumbled upon the GOPlot R package, developed by Wencke Walter and colleagues. The package provides some great tools for visualizing omics data. My favourite is the chord diagram, which captures the complex relationship between differential gene expression (shown on the left) and enriched functional categories (shown on the right)- here’s one I made for my ARVO conference poster this year:

The package is easy to use and provides a range of other plot options (bar plot, bubble plot, circle plot, cluster plot). I highly recommend you check it out!

6 comments:

  1. Hi Nina,
    how did you change the font? GOChord doesn't have and attribute for this

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  2. Hi Sergetto,
    I exported the vector image from R and edited the font and labels in Adobe Illustrator.

    Cheers,
    Nina

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  3. Hi Nina,

    I am using GOplot for visualizing my data. I am using an excel file that contains Genes and pathway along with fold change. But, I am getting error while ploting using GOchord function -

    Error - Error in `$<-.data.frame`(`*tmp*`, "x.start", value = c(0, 0.126527368920428, :
    replacement has 53 rows, data has 58

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  4. How do you change the color of the plot? I prefer your data settings.

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    Replies
    1. There is an argument inside GOChord called 'ribbon.col' where you can provide your own colors. The number of colors must be the same as the number of terms (GO terms). Code looks like this GOChord(data, ... , ribbon.col = 'your colors')

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  5. Hi Nina
    Your chord graph looks really nice and has no black border, do you know how to remove the black border?
    Would you please share you GOChord if it is possible?
    Many thanks

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