Function reference
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apl()
- Association Plot
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apl_coords()
- Calculate Association Plot coordinates
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apl_ggplot()
- Plot Association Plot with ggplot
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apl_plotly()
- Plot Association Plot with plotly
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apl_score()
- Find rows most highly associated with a condition
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apl_topGO()
- Run Gene overrepresentation analysis with topGO
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as.cacomp()
- Create cacomp object from Seurat/SingleCellExperiment container
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as.list(<cacomp>)
- Convert cacomp object to list.
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ca_3Dplot()
- Plot of the first 3D CA projection of the data.
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ca_biplot()
- Plot of 2D CA projection of the data.
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ca_coords()
- Calculate correspondence analysis row and column coordinates.
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new_cacomp()
- An S4 class that contains all elements needed for CA.
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cacomp()
- Correspondance Analysis
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cacomp_names()
- Prints slot names of cacomp object
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cacomp_slot()
- Access slots in a cacomp object
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check_cacomp()
- Check if cacomp object was correctly created.
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comp_std_residuals()
- Compute Standardized Residuals
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elbow_method()
- Runs elbow method
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is.empty()
- Helper function to check if object is empty.
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pick_dims()
- Compute statistics to help choose the number of dimensions
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plot_enrichment()
- Generates plot for results from apl_topGO
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recompute()
- Recompute missing values of cacomp object.
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rm_zeros()
- removes 0-only rows and columns in a matrix.
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runAPL()
- Compute and plot Association Plot
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run_cacomp()
- Internal function for `cacomp`
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scree_plot()
- Scree Plot
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show.cacomp()
show(<cacomp>)
- Prints cacomp object
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subset_dims()
- Subset dimensions of a caobj
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var_rows()
- Find most variable rows