`ValueError` from the `matplotlib` backend about dnafeaturesviewer HOT 8 CLOSED

Great, happy I could be of some help! Let me know if you run into any other trouble.

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The sequence_length parameter must always be the length of the full sequence. Originally you had entered 100 (now it is start - end). What happens then is that Matplotlib understands that 100 nucleotides corresponds to the whole 10 inches of the figure width (which you provide with figure_width=10) so if the feature locations have indices like 10000, Matplotlib will attempt to create a figure with a width of 1000 inches (that's huge!) just to represent the index 10000. As this is way too many pixels, this gives you the error you observe.

If you want to only plot a part of a figure, have a look at the section about cropping in the README:

https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer#nucleotide-sequences-translations-and-cropping

EDIT: typos

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Thanks for getting back to me so quickly. Is this only for plotting very small sequences? Is there any way to autodetect the sequence_length and adjust accordingly with figure_width?

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To be clear, my point was that if you set figure_width=10 you are guaranteed to have a 10 inch wide figure whatever the sequence length, it will auto-adjust and there will be no problems.

In your script, a problem appears for a particular reason, which is that you set sequence_length=100 but some of your features have locations very much outside the 0-100 interval, which certainly isn't intended.

Can you quickly describe what the purpose of the script is? I might help me point you in the right direction.

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I'm trying to plot gene neighborhoods around a particular locus so I was going to try ~10 genes up and downstream of a gene in Alteromonas macleodii

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Then I think you should use a cropped record:

record = GraphicRecord(sequence_length=10000, # anything big
                       features=features)
cropped_record = record.crop((START, END))
cropped_record.plot(figure_width=10)

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I just noticed you used figure_width=100 now. This means a figure of 100 inches (=2.5 meters) in width! You should keep it to 10 inches (figure_width=10).

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Haha, yea a 2.5 meter figure is a little much for what I was trying to do. Thank you so much for responding! I was almost about to recreate the wheel and was very bummed out b/c your figures already look so good.

I ended up using this edit that you suggested

sequence_length = 4653851
features = list()
positions = list()
pad = 10
for k in range(-n_peripheral, n_peripheral+1):
    data = df_gff3.iloc[loc_target+k]
    start = int(data["pos_start"])
    end = int(data["pos_end"])
    strand = {"+":+1, "-":-1}[data["sense"]]
    label = data["locus_tag"]
    feature = GraphicFeature(start=start, end=end, strand=strand, label=label)
    features.append(feature)
    positions += [start, end]
record = GraphicRecord(sequence_length=sequence_length, features=features).crop((min(positions)-pad, max(positions)+pad))
record.plot(figure_width=10)

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