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Teichlab / cellphonedb

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Having trouble using the function cellphonedb plot #129

Closed daisyyr closed 4 years ago

daisyyr commented 5 years ago

**It's my first time to use cellphonedb. I have no problem using cellphonedb method. While I was using cellphonedb plot with the code "cellphonedb plot dot-plot "

It showed errors as follows:**

R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/.

As there is no R environment set up, some functionalities will be disabled, e.g. plot R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/.

You cannot perform this plot command unless there is a working R setup according to CellPhoneDB specs

So what can I do with this situation? I have already installed R (version 3.6.1) Thanks~

keenhl commented 4 years ago

Do you know if you have the package ggplot2 installed in R?

CharleneZ95 commented 4 years ago

Set environment for R solved this, 

export PATH=/path/to/R/:$PATH
cellphonedb plot dot_plot --rows in/rows.txt --columns in/columns.txt

Hope this helps~

mvento commented 4 years ago

@daisyyr Did you fix this issue?

If it didn't work well, you can try to use this docker image https://hub.docker.com/r/ydevs/cellphonedb

Best