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plot: Visualize and Interact with Principal Coordinates Analysis Plots¶
Docstring:
Usage: qiime emperor plot [OPTIONS] Generates an interactive ordination plot where the user can visually integrate sample metadata. Inputs: --i-pcoa ARTIFACT The principal coordinates matrix to be plotted. PCoAResults [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] --p-custom-axes TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional] --p-ignore-missing-samples / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False] --p-ignore-pcoa-features / --p-no-ignore-pcoa-features Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised. [default: False] Outputs: --o-visualization VISUALIZATION [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). --example-data PATH Write example data and exit. --citations Show citations and exit. --use-cache DIRECTORY Specify the cache to be used for the intermediate work of this action. If not provided, the default cache under $TMP/qiime2/will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster. --help Show this message and exit. Examples: # ### example: emperor plot qiime emperor plot \ --i-pcoa pcoa-result.qza \ --m-metadata-file sample-metadata.tsv \ --o-visualization plot.qzv
Import:
from qiime2.plugins.emperor.visualizers import plot
Docstring:
Visualize and Interact with Principal Coordinates Analysis Plots Generates an interactive ordination plot where the user can visually integrate sample metadata. Parameters ---------- pcoa : PCoAResults The principal coordinates matrix to be plotted. metadata : Metadata The sample metadata. custom_axes : List[Str], optional Numeric sample metadata columns that should be included as axes in the Emperor plot. ignore_missing_samples : Bool, optional This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. ignore_pcoa_features : Bool, optional Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised. Returns ------- visualization : Visualization