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wangke16 / MSMC-IM

A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC
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TypeError: stem() got an unexpected keyword argument 'c' #6

Closed biozzq closed 3 years ago

biozzq commented 3 years ago

Dear @wangke16

Thank you for your excellent tools. I want to use it to help me better interpret the results of MSMC2, however it failed when using following command. Please note that the command also generates two files: SEA-Wild-SEA-Dom.b1_1e-08.b2_1e-06.MSMC_IM.estimates.txt, SEA-Wild-SEA-Dom.b1_1e-08.b2_1e-06.MSMC_IM.fittingdetails.txt.

python /MSMC-IM/MSMC_IM.py -mu 2.5e-8 -p 1*2+20*1+1*2+1*3 -o /03.MSMC_IM/SEA-Wild-SEA-Dom --printfittingdetails --plotfittingdetails --xlog /02.MSMC/SEA-Wild-SEA-Dom.CCR

##############################################################################
/MSMC-IM/MSMC_IM.py:164: UserWarning: Attempted to set non-positive left xlim on a log-scaled axis.
Invalid limit will be ignored.
  plt.xlim(0, 2e5)
/MSMC-IM/MSMC_IM.py:170: UserWarning: Attempted to set non-positive left xlim on a log-scaled axis.
Invalid limit will be ignored.
  plt.xlim(0, 2e5)
/MSMC-IM/MSMC_IM.py:182: UserWarning: Attempted to set non-positive left xlim on a log-scaled axis.
Invalid limit will be ignored.
  plt.xlim(0, 2e5)
Traceback (most recent call last):
  File "/MSMC-IM/MSMC_IM.py", line 191, in <module>
    plt.stem(xVec, yVec, linefmt=':', c='orange')
TypeError: stem() got an unexpected keyword argument 'c'

Sincerely, Zheng zhuqing

stschiff commented 3 years ago

OK, I think in order for @wangke16 to reproduce this you should send her your input data...

biozzq commented 3 years ago

Hi @wangke16

I attached the CCR file here, and the command I used is as follows;

python ./MSMC-IM/MSMC_IM.py -mu 2.5e-8 -p 1*2+20*1+1*2+1*3 -o ./out/SEA-Wild-SEA-Dom --printfittingdetails --plotfittingdetails --xlog SEA-Wild-SEA-Dom.CCR.txt

SEA-Wild-SEA-Dom.CCR.txt

Best regards,

wangke16 commented 3 years ago

Hi Zhuqing,

it’s a python plotting issue. I have fixed it. Please try again. TypeError should be gone now and you will get your fitting details in the output PDF file.

Best.

On 22 Jun 2021, at 14:43, biozzq @.***> wrote:

Hi @wangke16 https://github.com/wangke16 I attached the CCR file here, and the command I used is as follows;

python ./MSMC-IM/MSMC_IM.py -mu 2.5e-8 -p 12+201+12+13 -o ./out/SEA-Wild-SEA-Dom --printfittingdetails --plotfittingdetails --xlog SEA-Wild-SEA-Dom.CCR.txt

SEA-Wild-SEA-Dom.CCR.txt https://github.com/wangke16/MSMC-IM/files/6694266/SEA-Wild-SEA-Dom.CCR.txt Best regards,

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biozzq commented 3 years ago

Hi @wangke16

Thank you, it is ok now.

Best.