稀疏计数数据的鲁棒aitchison张量分解
gemelli的Python项目详细描述
gemelli仍在开发中，因此可能会发生向后不兼容的更改。如果您有任何问题，请随时联系eng.ucsd.edu的cmartino开发团队。
杰梅利
Gemelli是一个工具箱，用于在稀疏的组合组学数据集上运行张量分解。Gemelli对时空微生物群数据进行无监督降维。gemelli的outlut有助于解决时空主体的变异及其分离的生物学特征。
安装
要安装最新版本的deicode，请运行以下命令
# pip (only supported for QIIME2 >= 2018.8)
pip install gemelli
注意：gemelli与python 2不兼容，并且与python 3.4或更高版本兼容。
在QIIME 2
中使用gemelli可以找到qiime2教程here。
Note: a more formal tutorial is coming soon.
$qiime gemelli ctf --help Usage: qiime gemelli ctf [OPTIONS] Gemelli resolves spatiotemporal subject variation and the biological features that separate them. In this case, a subject may have several paired samples, where each sample may be a time point. The output is akin to conventional beta-diversity analyses but with the paired component integrated in the dimensionality reduction. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Input table in biom format. [required] Parameters: --m-sample-metadata-file METADATA... (multiple Sample metadata file in QIIME2 formatting. arguments will be merged)[required] --p-individual-id-column TEXT 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. [required] --p-state-column TEXT 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. [required] --p-n-components INTEGER The underlying low-rank structure (suggested: 2 < rank < 10)[minimum 2][default: 3] --p-min-sample-count INTEGER Minimum sum cutoff of sample across all features [default: 0] --p-min-feature-count INTEGER Minimum sum cutoff of features across all samples [default: 0] --p-max-iterations-als INTEGER Max number of Alternating Least Square (ALS) optimization iterations (suggested to be below 100; beware of overfitting)[minimum 1][default: 25] --p-max-iterations-rptm INTEGER Max number of Robust Tensor Power Method (RTPM) optimization iterations (suggested to be below 100; beware of overfitting)[minimum 1][default: 25] --p-n-initializations INTEGER The number of initialization vectors. Larger values willgive more accurate factorization but will be more computationally expensive [minimum 1][default: 25] --m-feature-metadata-file METADATA... (multiple arguments will be merged)[optional] Outputs: --o-subject-biplot ARTIFACT PCoAResults % Properties('biplot') 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. [required] --o-state-distance-matrix ARTIFACT DistanceMatrix A sample-sample distance matrix generated from the euclidean distance of the subject-state ordinations and itself. [required] --o-state-subject-ordination ARTIFACT SampleData[SampleTrajectory] A trajectory is an ordination that can be visualizedover time or another context. [required] --o-state-feature-ordination ARTIFACT FeatureData[FeatureTrajectory] A trajectory is an ordination that can be visualizedover time or another context. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --citations Show citations and exit. --help Show this message and exit.
将Gemelli用作独立工具
$ gemelli cmartino$ gemelli --help Usage: gemelli [OPTIONS] Runs CTF with an rclr preprocessing step. Options: --in-biom TEXT Input table in biom format. [required] --sample-metadata-file TEXT Sample metadata file in QIIME2 formatting. [required] --individual-id-column TEXT 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. [required] --state-column-1 TEXT 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. [required] --output-dir TEXT Location of output files. [required] --n_components INTEGER The underlying low-rank structure (suggested: 1 < rank < 10)[minimum 2][default: 3] --min-sample-count INTEGER Minimum sum cutoff of sample across all features [default: 0] --min-feature-count INTEGER Minimum sum cutoff of features across all samples [default: 5] --max_iterations_als INTEGER Max number of Alternating Least Square (ALS) optimization iterations (suggested to be below 100; beware of overfitting)[minimum 1][default: 50] --max_iterations_rptm INTEGER Max number of Robust Tensor Power Method (RTPM) optimization iterations (suggested to be below 100; beware of overfitting)[minimum 1][default: 50] --n_initializations INTEGER The number of initialization vectors. Larger values willgive more accurate factorization but will be more computationally expensive (suggested to be below 100; beware of overfitting)[minimum 1][default: 50] --feature-metadata-file TEXT Feature metadata file in QIIME2 formatting. --state-column-2 TEXT 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. --state-column-3 TEXT 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. --state-column-4 TEXT 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. --help Show this message and exit.
其他资源
以阿利吉耶罗·博埃蒂和意大利面食命名。
TenAls translated from Sewoong Oh
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