Association Plots

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Documentation for package ‘APL’ version 1.11.2

• 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