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.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.
ca_coords               Calculate correspondence analysis row and
                        column coordinates.
cacomp                  Correspondance Analysis
cacomp_names            Prints slot names of cacomp object
cacomp_slot             Access slots in a cacomp object
cacomp-class            An S4 class that contains all elements needed
                        for CA.
calc_residuals          Calculate residuals for Correspondence analysis
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.
permutation_cutoff      Calculates permuted association plot
                        coordinates
pick_dims               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.
run_APL                 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
