Input: fasta file that has been already aligned by user. Will contain multiple datasets(For now just 2)
output: PCA 3D graphics showing difference of dataset
Need to determine best way to allow user to supply different datasets to be compared. Right now, all sequence names have a common name for the dataset
See https://github.com/VDBWRAIR/bio_pieces/blob/pca/tests/testinput/aln1.fasta
This file has 2 data sets that need to be compared. Essentially, the graphic needs to have 2 colors to distinquish them
Currently the script aln_pca builds what I think is a PCA graphic(https://github.com/VDBWRAIR/bio_pieces/blob/pca/docs/_static/pca.png), however, I am not 100% confident it is done correctly as the matplotlib and scikit-learn PCA graphics look different.
You can also check out www.jalview.org as it builds a PCA graphic that we are trying to semi-replicate, but with better colors and axis and such.
The pca branch also includes a hacked together ipython notebook for messing around with which has the matplotlib as well as scikit-learn pca graphic which you can see does not look like the manual one I built using the tutorial from a different website which is listed in that file.
@mmelendrez
@averagehat
Input: fasta file that has been already aligned by user. Will contain multiple datasets(For now just 2)
output: PCA 3D graphics showing difference of dataset
Need to determine best way to allow user to supply different datasets to be compared. Right now, all sequence names have a common name for the dataset
See https://github.com/VDBWRAIR/bio_pieces/blob/pca/tests/testinput/aln1.fasta
This file has 2 data sets that need to be compared. Essentially, the graphic needs to have 2 colors to distinquish them
Currently the script
aln_pcabuilds what I think is a PCA graphic(https://github.com/VDBWRAIR/bio_pieces/blob/pca/docs/_static/pca.png), however, I am not 100% confident it is done correctly as the matplotlib and scikit-learn PCA graphics look different.You can also check out www.jalview.org as it builds a PCA graphic that we are trying to semi-replicate, but with better colors and axis and such.
The pca branch also includes a hacked together ipython notebook for messing around with which has the matplotlib as well as scikit-learn pca graphic which you can see does not look like the manual one I built using the tutorial from a different website which is listed in that file.
@mmelendrez
@averagehat