visomics low-level script

Copyright (C) 2022 Xia,Xiao-Qin

Contact

xqxia@ihb.ac.cn

detail infomation:
'''
Rversion1.R:Primarily performing R analysis, plotting scripts that have been fine-tuned
temp_domain.R:Perform protein domain mapping
cmd.sh:Perform protein structure predictions,Requires pfscam.pl and the corresponding pfscam database
ppi.py:To perform protein interaction calculations, you need to download stringDB data in advance
'''

usage
'''
In general, the first step to get calculation results and preliminary pictures, and then the second step to edit the pictures. If you don't need to edit pictures, just execute the first step. Considering that these scripts are used with a large number of parameters on the page, the configuration parameters may be very complicated, especially the second step's parameters may reach hundreds, if you need to adjust the map, please use the web page itself. We provide two examples to demonstrate:
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First step: Initial Analysis and Plotting
./Rversion1.x.R de_analyse 11 ./deanalysis/data_deanalysis 0 ./deanalysis/feature_deanalysis > ./deanalysis/err.txt 2>&1 &
or 
./Rversion1.x.R ordinations 11 ./ordinations/data_ordinations 0 ./ordinations/feature_ordinations >./ordinations/err.txt 2>&1 &
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Second step: Modify the picture when the first step is successful
./Rversion1.x.R 0 01 0 ./deanalysis/user.conf_deanalysis > ./deanalysis/err_01.txt 2>&1 &
or
./Rversion1.x.R 0 01 0 ./ordinations/user.conf_ordinations >./ordinations/err_01.txt 2>&1 &
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***
Note:
1. Rversion1.x.R 'x' represents the version, pay attention to modify the corresponding number under the compressed package when running.
2. Before running Rversion1.x.R, please replace the Rscript in the first line with the R path on your computer. Please make sure that your R has installed the R package specified in the script.
3. In fact, the sample files required by different functions can be downloaded on the page, and the data required during operation is actually a file without suffix separated by "\t" corresponding to the sample file. Take the ./ordinations/data_ordinations input as an example, which is actually a sample file available for download in the ordinations section of the page (http://bioinfo.ihb.ac.cn/dj_static/GBTP/magicRversion1/download/ordinations.txt).
***

feature: First step's parameter configuration file
The "out" key value is the folder path corresponding to the input file.
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user.conf: Second step's parameter configuration file
The "out" key value is the output directory corresponding to the first step.
'''
