CompassAnalyzer: CompassAnalyzer
In YosefLab/compassR: A Library for Conducting Analyses on COMPASS Data
Description
Public fields
Methods
Description
An object through which you can access several useful functions for your COMPASS analysis.
Public fields
settingsThe CompassSettings instance specifying the settings for this CompassAnalyzer instance.
Methods
Public methods
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Method new()
Initialize the CompassAnalyzer instance.
Usage
CompassAnalyzer$new(settings)
Arguments
settingsThe CompassSettings instance specifying the settings for this CompassAnalyzer instance.
Returns
NULL.
Method print()
Prints a human-readable representation of this CompassAnalyzer instance.
Usage
CompassAnalyzer$print(...)
Arguments
...Unused.
Returns
NULL.
Method repr()
Returns a human-readable representation of this CompassAnalyzer instance.
Usage
CompassAnalyzer$repr(...)
Arguments
...Unused.
Returns
An output.
Method conduct_wilcoxon_test()
Description.
Usage
CompassAnalyzer$conduct_wilcoxon_test(
consistencies_matrix,
group_A_cell_ids,
group_B_cell_ids,
...,
for_metareactions = TRUE
)
Arguments
consistencies_matrixEither your CompassData instance's reaction_consistencies matrix, or its metareaction_consistencies matrix, depending on whether you want a table whose rows correspond to reactions or metareactions.
group_A_cell_idsA character vector containing the IDs of the cells that constitute group A.
group_B_cell_idsA character vector containing the IDs of the cells that constitute group B.
...Unused.
for_metareactionsWhether the first argument is your reaction_consistencies matrix or your metareaction_consistencies matrix. This argument doesn't affect the contents of the returned tibble, but merely ensures that its column names are appropriate.
Returns
A tibble, where each row represents a Wilcoxon rank-sum test for whether a reaction or metareaction achieves a higher consistency among the group A cells than among the group B cells. It has the following columns: reaction_id or metareaction_id, wilcoxon_statistic, cohens_d, p_value, and adjusted_p_value.
Method get_umap_components()
Description.
Usage
CompassAnalyzer$get_umap_components(
consistencies_matrix,
...,
num_components = 2
)
Arguments
consistencies_matrixEither your CompassData instance's reaction_consistencies matrix, or its metareaction_consistencies matrix, depending on whether the high-dimensional representation of each cell should encapsulate the cell's reaction consistencies or its metareaction consistencies. In the former case the UMAP algorithm will find a num_components-dimensional embedding for each cell in (# reactions)-dimensional space, and in the latter case the UMAP algorithm will find a num_components-dimensional embedding for each cell in (# metareactions)-dimensional space.
...Unused.
num_componentsThe number of UMAP components to calculate (i.e. the dimensionality of the embedding).
Returns
A tibble, where each row represents the low-dimensional UMAP embedding of a cell. It has the following columns: Your CompassSettings instance's cell_id_col_name, component_1, component_2, ..., component_num_components.
Method clone()
The objects of this class are cloneable with this method.
Usage
CompassAnalyzer$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
YosefLab/compassR documentation built on May 3, 2021, 7:31 a.m.
R Package Documentation
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Description Public fields Methods
Description
An object through which you can access several useful functions for your COMPASS analysis.
Public fields
settingsThe CompassSettings instance specifying the settings for this CompassAnalyzer instance.
Methods
Public methods
Method new()
Initialize the CompassAnalyzer instance.
Usage
CompassAnalyzer$new(settings)
Arguments
settingsThe CompassSettings instance specifying the settings for this CompassAnalyzer instance.
Returns
NULL.
Method print()
Prints a human-readable representation of this CompassAnalyzer instance.
Usage
CompassAnalyzer$print(...)
Arguments
...Unused.
Returns
NULL.
Method repr()
Returns a human-readable representation of this CompassAnalyzer instance.
Usage
CompassAnalyzer$repr(...)
Arguments
...Unused.
Returns
An output.
Method conduct_wilcoxon_test()
Description.
Usage
CompassAnalyzer$conduct_wilcoxon_test( consistencies_matrix, group_A_cell_ids, group_B_cell_ids, ..., for_metareactions = TRUE )
Arguments
consistencies_matrixEither your CompassData instance's reaction_consistencies matrix, or its metareaction_consistencies matrix, depending on whether you want a table whose rows correspond to reactions or metareactions.
group_A_cell_idsA character vector containing the IDs of the cells that constitute group A.
group_B_cell_idsA character vector containing the IDs of the cells that constitute group B.
...Unused.
for_metareactionsWhether the first argument is your reaction_consistencies matrix or your metareaction_consistencies matrix. This argument doesn't affect the contents of the returned tibble, but merely ensures that its column names are appropriate.
Returns
A tibble, where each row represents a Wilcoxon rank-sum test for whether a reaction or metareaction achieves a higher consistency among the group A cells than among the group B cells. It has the following columns: reaction_id or metareaction_id, wilcoxon_statistic, cohens_d, p_value, and adjusted_p_value.
Method get_umap_components()
Description.
Usage
CompassAnalyzer$get_umap_components( consistencies_matrix, ..., num_components = 2 )
Arguments
consistencies_matrixEither your CompassData instance's reaction_consistencies matrix, or its metareaction_consistencies matrix, depending on whether the high-dimensional representation of each cell should encapsulate the cell's reaction consistencies or its metareaction consistencies. In the former case the UMAP algorithm will find a num_components-dimensional embedding for each cell in (# reactions)-dimensional space, and in the latter case the UMAP algorithm will find a num_components-dimensional embedding for each cell in (# metareactions)-dimensional space.
...Unused.
num_componentsThe number of UMAP components to calculate (i.e. the dimensionality of the embedding).
Returns
A tibble, where each row represents the low-dimensional UMAP embedding of a cell. It has the following columns: Your CompassSettings instance's cell_id_col_name, component_1, component_2, ..., component_num_components.
Method clone()
The objects of this class are cloneable with this method.
Usage
CompassAnalyzer$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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