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Merge pull request #16 from cameronmartino/command-line
Command line and QIIME2 -- refactoring
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# Configuration file where you can set the parameter default values and | ||
# descriptions. | ||
DEFAULT_COMP = 3 | ||
DEFAULT_MSC = 0 | ||
DEFAULT_MFC = 0 | ||
DEFAULT_MAXITER = 25 | ||
DEFAULT_FMETA = None | ||
DEFAULT_COND = None | ||
|
||
DESC_INIT = ("The number of initialization vectors. Larger values will" | ||
"give more accurate factorization but will be more " | ||
"computationally expensive [minimum 1]") | ||
DESC_ITERATIONSALS = ("Max number of Alternating Least Square (ALS)" | ||
" optimization iterations (suggested to be below 100;" | ||
" beware of overfitting) [minimum 1]") | ||
DESC_ITERATIONSRTPM = ("Max number of Robust Tensor Power Method (RTPM)" | ||
" optimization iterations (suggested to be below 100;" | ||
" beware of overfitting) [minimum 1]") | ||
DESC_COMP = ("The underlying low-rank structure (suggested: 2 < rank < 10)" | ||
" [minimum 2]") | ||
DESC_MSC = "Minimum sum cutoff of sample across all features" | ||
DESC_MFC = "Minimum sum cutoff of features across all samples" | ||
DESC_OUT = "Location of output files." | ||
DESC_FMETA = "Feature metadata file in QIIME2 formatting." | ||
DESC_BIN = "Input table in biom format." | ||
DESC_SMETA = "Sample metadata file in QIIME2 formatting." | ||
DESC_SUBJ = ("Metadata column containing subject IDs to" | ||
" use for pairing samples. WARNING: if" | ||
" replicates exist for an individual ID at" | ||
" either state_1 to state_N, that subject will" | ||
" be mean grouped by default.") | ||
DESC_COND = ("Metadata column containing state (e.g.,Time, BodySite)" | ||
" across which samples are paired." | ||
" At least one is required but up to four are allowed" | ||
" by other state inputs.") | ||
QORD = ("A trajectory is an ordination that can be visualized" | ||
"over time or another context.") | ||
QDIST = ("A sample-sample distance matrix generated from the euclidean distance" | ||
" of the subject-state ordinations and itself.") | ||
QLOAD = ("Compositional biplot of subjects as points and features as arrows." | ||
" Where the variation between subject groupings is explained by the" | ||
" log-ratio between opposing arrows. WARNING: The % variance explained" | ||
" is spread over n_components and can be inflated.") |
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@article {Martino2019, | ||
author = {Martino, Cameron and Morton, James T. and Marotz, Clarisse A. and Thompson, Luke R. and Tripathi, Anupriya and Knight, Rob and Zengler, Karsten}, | ||
editor = {Neufeld, Josh D.}, | ||
title = {A Novel Sparse Compositional Technique Reveals Microbial Perturbations}, | ||
volume = {4}, | ||
number = {1}, | ||
elocation-id = {e00016-19}, | ||
year = {2019}, | ||
doi = {10.1128/mSystems.00016-19}, | ||
publisher = {American Society for Microbiology Journals}, | ||
URL = {https://msystems.asm.org/content/4/1/e00016-19}, | ||
eprint = {https://msystems.asm.org/content/4/1/e00016-19.full.pdf}, | ||
journal = {mSystems} | ||
} |
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