Man pages for ClemensKohl/APL
Association Plots

aplAssociation Plot
apl_coordsCalculate Association Plot coordinates
apl_ggplotPlot Association Plot with ggplot
apl_plotlyPlot Association Plot with plotly
apl_scoreFind rows most highly associated with a condition
apl_topGORun Gene overrepresentation analysis with topGO
as.cacompCreate cacomp object from Seurat/SingleCellExperiment...
as.list-cacomp-methodConvert cacomp object to list.
ca_3DplotPlot of the first 3D CA projection of the data.
ca_biplotPlot of 2D CA projection of the data.
cacompCorrespondance Analysis
cacomp-classAn S4 class that contains all elements needed for CA.
cacomp_namesPrints slot names of cacomp object
cacomp_slotAccess slots in a cacomp object
ca_coordsCalculate correspondence analysis row and column coordinates.
calc_residualsCalculate residuals for Correspondence analysis
check_cacompCheck if cacomp object was correctly created.
clip_residualsPerform clipping of residuals
comp_ft_residualsCompute Freeman-Tukey residuals
comp_NB_residualsCompute Negative-Binomial residuals
comp_std_residualsCompute Standardized Residuals
elbow_methodRuns elbow method
inertia_rowsFind most variable rows
is.emptyHelper function to check if object is empty.
permutation_cutoffCalculates permuted association plot coordinates
pick_dimsCompute statistics to help choose the number of dimensions
pipePipe operator
plot_enrichmentGenerates plot for results from apl_topGO
random_direction_cutoffRandom direction association plot coordinates
recomputeRecompute missing values of cacomp object.
rm_zerosremoves 0-only rows and columns in a matrix.
runAPLCompute and plot Association Plot
run_cacompInternal function for 'cacomp'
scree_plotScree Plot
show.cacompPrints cacomp object
sub-cacomp-ANY-ANY-ANY-methodSubset rows and columns of a cacomp object.
subset_dimsSubset dimensions of a caobj
var_rowsFind most variable rows
ClemensKohl/APL documentation built on Dec. 31, 2022, 8:13 a.m.