Association Plots

apl | Association Plot |

apl_coords | Calculate Association Plot coordinates |

apl_score | Find rows most highly associated with a condition |

apl_topGO | Run Gene overrepresentation analysis with topGO |

as.cacomp | Create cacomp object from Seurat/SingleCellExperiment... |

as.list-cacomp-method | Convert cacomp object to list. |

ca_3Dplot | Plot of the first 3 CA dimensions. |

ca_biplot | Plot of the first 2 CA dimensions. |

cacomp | Correspondance Analysis |

cacomp-class | An S4 class that contains all elements needed for CA. |

ca_coords | Calculate correspondence analysis row and column coordinates. |

check_cacomp | Check if cacomp object was correctly created. |

comp_std_residuals | Compute Standard Residuals |

is.empty | Helper function to check if object is empty. |

pick_dims | Compute statistics to help choose the number of dimensions |

pipe | Pipe operator |

plot_enrichment | Generates plot for results from apl_topGO |

recompute | Recompute missing values of cacomp object. |

rm_zeros | removes 0-only rows and columns in a matrix. |

runAPL | Compute and plot Association plot |

run_cacomp | Internal function for 'cacomp' |

scree_plot | Scree Plot |

show.cacomp | Prints cacomp object |

subset_dims | Subset dimensions of a caobj |

var_rows | Find most variable rows |

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