# Association Plots

## Documentation for package ‘APL’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 container
as.cacomp-method | Create cacomp object from Seurat/SingleCellExperiment container
as.list-method | Convert cacomp object to list.
cacomp | Correspondance Analysis
cacomp-class | An S4 class that contains all elements needed for CA.
cacomp-method | Correspondance Analysis
cacomp_names | Prints slot names of cacomp object
cacomp_slot | Access slots in a cacomp object
calc_residuals | Calculate residuals for Correspondence analysis
ca_3Dplot | Plot of the first 3D CA projection of the data.
ca_3Dplot-method | Plot of the first 3D CA projection of the data.
ca_biplot | Plot of 2D CA projection of the data.
ca_biplot-method | Plot of 2D CA projection of the data.
ca_coords | Calculate correspondence analysis row and column coordinates.
check_cacomp | Check if cacomp object was correctly created.
clip_residuals | Perform clipping of residuals
comp_ft_residuals | Compute Freeman-Tukey residuals
comp_NB_residuals | Compute Negative-Binomial residuals
comp_std_residuals | Compute Standardized Residuals
elbow_method | Runs elbow method
inertia_rows | Find most variable rows
is.empty | Helper function to check if object is empty.
new_cacomp | An S4 class that contains all elements needed for CA.
permutation_cutoff | Calculates permuted association plot coordinates
pick_dims | Compute statistics to help choose the number of dimensions
pick_dims-method | Compute statistics to help choose the number of dimensions
plot_enrichment | Generates plot for results from apl_topGO
random_direction_cutoff | Random direction association plot coordinates
recompute | Recompute missing values of cacomp object.
rm_zeros | removes 0-only rows and columns in a matrix.
runAPL | Compute and plot Association Plot
runAPL-method | Compute and plot Association Plot
run_APL | Compute and plot Association Plot
run_cacomp | Internal function for 'cacomp'
scree_plot | Scree Plot
show-method | Prints cacomp object
show.cacomp | Prints cacomp object
subset_dims | Subset dimensions of a caobj
var_rows | Find most variable rows