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ajitjohnson / imsig

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
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"plot_network" error #5

Closed immuneAI closed 5 years ago

immuneAI commented 5 years ago

Hey, I'm facing "Error in cor_data[fg, fg] : subscript out of bounds" error while using plot_network. Please help!

ajitjohnson commented 5 years ago

Hey Venkat,

Does the function work with the example dataset (attached with the package)? plot_network (exp = exp, r = 0.7)

If so, can you send me a snapshot of your data header?

head(data)

Thanks, Ajit.

immuneAI commented 5 years ago

example dataset works brilliant!

head(nexp) AB..9869 MIST16 MIST18 MIST1 MIST25 MIST33 MIST34 MIST35 MIST42 MIST45 MIST46 MIST56 MIST58 TSPAN6 4.96 1.35 5.26 1.19 3.28 2.38 6.51 1.36 1.77 2.38 1.53 0.36 1.51 TNMD 0.00 0.03 0.09 0.02 0.00 0.01 2.47 0.09 0.02 0.00 0.00 0.00 0.00 DPM1 8.39 2.87 7.62 4.40 4.01 5.64 8.88 7.74 4.08 10.21 1.80 0.76 3.18 SCYL3 1.27 1.07 1.79 1.11 1.06 1.17 1.58 1.12 1.68 1.44 0.54 0.34 0.51 C1orf112 1.94 0.64 2.63 0.77 0.77 1.07 2.00 1.37 0.47 0.74 0.59 0.26 0.37 FGR 0.21 4.16 1.29 1.14 3.11 1.95 0.98 3.14 0.49 13.13 0.47 1.08 0.56

ajitjohnson commented 5 years ago

It looks fine. Do the other functions work?
gene_stat (exp = nexp, r = 0.7) or imsig (exp = nexp, r = 0.7)
Also try checking if there any duplicates in your rownames.

JoKPro commented 3 years ago

Hello! I am having the same problem, everything works fine until plot_network.

Unbenannt

Would love to hear back from you!