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I have some gene expression data in different parts of plant roots (see the image) and I want to show the gene expression levels in different parts of the roots. For example, if the gene is highly expressed in the apical meristem, I want to mark the apical meristem part of the schematic diagram red. One possibility is to make the diagram a map, does anyone have any suggestion how to make a diagram to a map in R? Or if you know any tool for this purpose, please let me know. Thank you!

The plant root structure

l0110
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  • SO only accepts raster image files, but if your original has actual structure you could color individual polygons. – IRTFM Jun 08 '16 at 17:56

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You could draw your own polygons to separate the regions using the raster package. Or, this post may provide a better way to do this.

Then, you can create a heat map and color within the polygons. Say, with ggplot2::geom_polygon()

To make it look even better, you could use the original image as a background, and then overlay your heat map with some transparency (i.e. the alpha argument in ggplot2) so you can see the colored heat map and some of the original image. See this post for more details, or this post if you like funny pictures

Community
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BarkleyBG
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  • Thanks so much, BarkelyBG! The human body post is the one I need since I have a SVG file for cell shape. – l0110 Jun 09 '16 at 15:51