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GOCircle error #4

Closed MARGINMB closed 7 years ago

MARGINMB commented 7 years ago

When running GOCircle on the circ object, I get the following error. Error in stats::runif(scount[sc], df$x[sc] + 0.06, (df$x[sc] + df$xmax[sc] - : invalid arguments The circ object looks fine so I am not sure what the problem really is.

head(circ) category ID term count genes logFC adj_pval zscore 1 MF GO:0001071 nucleic acid binding transcription factor activity 52 ZNF717 -0.864365 6.09e-11 1.38675 2 MF GO:0001071 nucleic acid binding transcription factor activity 52 NR2C1 -0.316350 6.09e-11 1.38675 3 MF GO:0001071 nucleic acid binding transcription factor activity 52 ZBTB38 -0.462620 6.09e-11 1.38675 4 MF GO:0001071 nucleic acid binding transcription factor activity 52 ZNF184 0.704550 6.09e-11 1.38675 5 MF GO:0001071 nucleic acid binding transcription factor activity 52 ZNF189 0.486880 6.09e-11 1.38675 6 MF GO:0001071 nucleic acid binding transcription factor activity 52 ZKSCAN8 -0.393590 6.09e-11 1.38675

Would appreciate your support. Thank you!

wencke commented 7 years ago

Could you please tell me the exact comment you used (with all parameters)?

MARGINMB commented 7 years ago

GOCircle(circ,label.size=3) No error was produced though after running install_github('wencke/wencke.github.io'). It might have been an issue with the development version I previously used.

MARGINMB commented 7 years ago

Dear Wencke,

When plotting a specific set of GO terms using GOCircle, as all terms have positive Z-score, the Z-score scale is a gradient of red (decreasing to increasing). I would like to have, if possible, a gradient of blue (for negative values), white, and red (for positive values), even though I do not have any terms with Z-score below 0. I have tried to specify that in the zsc.col vector but it did not work. Would appreciate advice on that.

Also, is there any way I can use the actual term description for the circle radius segments instead of the IDs? I have tried to generate a table with circle_dat where I did not input any IDs, only the actual terms descriptions, but then I got the following error when running GOCircle(circ):

Error in data.frame(x = seq(0, 10 - (10/N), length = N), xmax = rep(10/N - : arguments imply differing number of rows: 5, 0

Thank you in advance.

Kind regards,

Michael

On Mon, Feb 6, 2017 at 9:47 AM, Wencke Walter notifications@github.com wrote:

Could you please tell me the exact comment you used (with all parameters)?

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caonetto commented 3 years ago

I am getting the exact same issue when running Gocirc Error in stats::runif(scount[sc], df$x[sc] + 0.06, (df$x[sc] + df$xmax[sc] - :

Any ideas?

Lolowation commented 1 year ago

Me too have the sameerror

paolabc commented 1 year ago

Hi Everyone

I also have the same issue. It seems that is occurs when the data only contains positive zscores. Did someone knows how to solve it?

Thanks, Paola

santoshdbhosale commented 7 months ago

Hello Everyone,

Does anyone happen to tackle the following issue? Error in stats::runif(scount[sc], df$x[sc] + 0.06, (df$x[sc] + df$xmax[sc] - : invalid arguments Thanks, Santosh

Nhien198 commented 7 months ago

Thank you very much for your email!I am not online now, I will reply you as soon as possible.Best wish, 

permishen commented 5 months ago

GOCircle(circ_mf) Error in stats::runif(scount[sc], df$x[sc] + 0.06, (df$x[sc] + df$xmax[sc] - : Does anyone happen to tackle the following issue?

Nhien198 commented 5 months ago

Thank you very much for your email!I am not online now, I will reply you as soon as possible.Best wish,