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All functions

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>)
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.
new_cacomp()
An S4 class that contains all elements needed for CA.
cacomp()
Correspondance Analysis
cacomp_names()
Prints slot names of cacomp object
cacomp_slot()
Access slots in a cacomp object
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
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_cacomp()
Internal function for `cacomp`
scree_plot()
Scree Plot
show.cacomp() show(<cacomp>)
Prints cacomp object
subset_dims()
Subset dimensions of a caobj
var_rows()
Find most variable rows