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reneshbedre / bioinfokit

Bioinformatics data analysis and visualization toolkit
MIT License
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module 'bioinfokit.visuz' has no attribute 'GeneExpression' #44

Closed daschukds closed 2 years ago

daschukds commented 2 years ago

Hi.

Thanks for sharing nice scripts. Recently I wanted to make volcano plot. However I got this error "module 'bioinfokit.visuz' has no attribute 'GeneExpression'

I updated the bioinfokit. but no success.

Could you let me know what's happening? I am using python (ver 3.7 or 3.8) on Windows 10 home version.

update: I just installed it in windows command line window by : pip install bioinfokit It installed v 0.6.xxxx updated it pip --upgrade bioinfokit Here is the error screen below

======================================================================= Requirement already satisfied: bioinfokit in c:\programdata\anaconda3\lib\site-packages (0.6) Collecting bioinfokit Using cached bioinfokit-2.0.8.tar.gz (84 kB) ERROR: Command errored out with exit status 1: command: 'C:\ProgramData\Anaconda3\python.exe' -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\xxx\AppData\Local\Temp\pip-install-421w2xln\bioinfokit_579b051cf380446c8f48ff558d85d896\setup.py'"'"'; file='"'"'C:\Users\xxx\AppData\Local\Temp\pip-install-421w2xln\bioinfokit_579b051cf380446c8f48ff558d85d896\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\xxx\AppData\Local\Temp\pip-pip-egg-info-xg3tboln' cwd: C:\Users\xxx\AppData\Local\Temp\pip-install-421w2xln\bioinfokit_579b051cf380446c8f48ff558d85d896\ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "C:\Users\xxx\AppData\Local\Temp\pip-install-421w2xln\bioinfokit_579b051cf380446c8f48ff558d85d896\setup.py", line 5, in long_description = fh.read() UnicodeDecodeError: 'cp949' codec can't decode byte 0xe2 in position 62525: illegal multibyte sequence

WARNING: Discarding https://files.pythonhosted.org/packages/8f/a5/e23716d25cb293873f64a372ae93e3d013da726838792f5d670b95562021/bioinfokit-2.0.8.tar.gz#sha256=6155ef2566b76b731c10d09ba2828941c619bc8a0a838ed21cd58d68cef90977 (from https://pypi.org/simple/bioinfokit/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Here is the code I used below.

=================================

import packages

import pandas as pd from bioinfokit import analys, visuz

import the DGE table (condition_infected_vs_control_dge.csv)

df = pd.read_csv("xxxxxxx/xxx_dge.csv")

drop NA values

df=df.dropna()

create volcano plot

visuz.GeneExpression.volcano(df=df, lfc='log2FoldChange', pv='padj', sign_line=True, plotlegend=True)

reneshbedre commented 2 years ago

Please check your bioinfokit version. If the version is lesser than v2.0.8, upgrade your bioinfokit version to the latest version. See this article to learn how to upgrade the current version https://www.reneshbedre.com/blog/install-upgrade-pip-windows-mac-linux.html

daschukds commented 2 years ago

Hi. I found the main reason of failure. It still fails. but I think you can close this issue.