Man pages for VingronLab/APL
Association Plots
| apl | Association Plot |
| apl_coords | Calculate Association Plot coordinates |
| apl_ggplot | Plot Association Plot with ggplot |
| apl_plotly | Plot Association Plot with plotly |
| 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 3D CA projection of the data. |
| ca_biplot | Plot of 2D CA projection of the data. |
| cacomp | Correspondance Analysis |
| cacomp-class | An S4 class that contains all elements needed for CA. |
| cacomp_names | Prints slot names of cacomp object |
| cacomp_slot | Access slots in a cacomp object |
| ca_coords | Calculate correspondence analysis row and column coordinates. |
| check_cacomp | Check if cacomp object was correctly created. |
| comp_std_residuals | Compute Standardized Residuals |
| elbow_method | Runs elbow method |
| 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_APL | Internal function to 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 |
