SickleJr-class {jrSiCKLSNMF} | R Documentation |
The SickleJr class
Description
Defines the SickleJr class for use with jrSiCKLSNMF. This object contains all of the information required for analysis using jrSiCKLSNMF. This includes count matrices, normalized matrices, graph Laplacians, hyperparameters, diagnostic plots, and plots of cell clusters.
Value
An object of class SickleJr
Slots
count.matrices
A list containing all of the quality controlled count matrices. Note that these count matrices should not use all features and should only include features that appear in at a minimum 10 cells.
normalized.count.matrices
A list that holds the normalized count matrices
graph.laplacian.list
A list of the graph Laplacians to be used for graph regularization
rowRegularization
A string that indicates the type of row regularization to use. Types include "None" and "L2Norm"
diffFunc
A string that holds the name of the function used to measure the discrepancy between data matrix X and WH for each modality; can be
"klp"
for the Poisson Kullback-Leibler divergence or"fr"
for the Frobenius normlambdaWlist
A list of lambda values to use as the hyperparameters for the corresponding
\mathbf{W}^v
in thev^{\text{th}}
modalitylambdaH
A numeric value corresponding to the hyperparameter of the sparsity constraint on
\mathbf{H}
Wlist
A list of the generated
\mathbf{W}^v
matrices, one for each modalityH
The shared
\mathbf{H}
matrixWHinitials
A list that if, when using
PlotLossvsLatentFactors
, all of the cells are used to calculate the initial values, stores these initial generated matrices; can be used as initializations when runningRunjrSiCKLSNMF
to save timelossCalcSubsample
A vector that holds the cell indices on which
PlotLossvsLatentFactors
was calculatedlatent.factor.elbow.values
A data frame that holds the relevant information to plot the latent factor elbow plot
minibatch
Indicator variable that states whether the algorithm should use mini-batch updates.
clusterdiagnostics
List of the cluster diagnostic results for the SickleJr object. Includes diagnostic plots from
fviz_nbclust
and and diagnostics fromclValid
clusters
List of results of different clustering methods performed on the SickleJr object
metadata
List of metadata
loss
Vector of the value for the loss function
umap
List of different UMAP-based dimension reductions using
umap
plots
Holds various
ggplot
results for easy access of diagnostics and cluster visualizations