Man pages for yanwu2014/swne
Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

AdjustVarianceAdjust feature variance to remove effect of varying feature...
CalcGenesetLoadingsCalculate geneset factor loadings from gene factor loadings
CalcSNNSNN Graph Construction. Adapted from Seurat.
CheckGeneEmbeddingValidates gene embeddings by plotting cluster logFC vs gene...
clean_genesetsHelper function for filtering genesets
ClusterIndicatorMatrixCreates a clusters x cells indicator matrix where a 1 means...
compute_projected_snnHelper function for calculating a SNN graph Adapted from...
EmbedContoursEmbeds data for generating elliptical contours to mark areas...
EmbedFeaturesEmbeds features relative to factor coordinates
EmbedGenesetsEmbeds genesets relative to factor coordinates
EmbedSWNEEmbeds NMF factors and samples in 2 dimensions
ExtractDebatchedSeuratReconstructs the gene expression matrix from the CCA gene...
ExtractFieldExtract a field from a delimited string
ExtractNormCountsExtracts scaled counts from Seurat or Pagoda2 objects
ExtractSWNEColorsExtracts the exact colors used to plot each cluster (the hex...
FactorAssociationFind the top gene or geneset markers for each NMF factor...
FeaturePlotDimsPlots 2d embedding with feature overlayed
FeaturePlotSWNEPlots swne embedding with feature overlayed
FilterDataFilter data by minimum cells, minimum genes, and winsorizes...
FilterGenesetsFilters genesets according to minimum and maximum set size
FindNumFactorsDetermines the optimal number of NMF factors to use by...
FlattenGroupsConvert list of sample groups into a flat vector. Removes all...
ft_transformFreeman-Tukey transform for variance stabilization
genesets_indicatorCreates a genes x genesets indicator matrix
get_factor_coordsCalculates the coordinates of the NMF factors via Sammon...
get_sample_coordsCalculate sample coordinates using the NMF scores and NMF...
ggHeatPlots a heatmap using ggplot2
ica_initIndependent component analysis initialization. Negative...
kl_divKL divergence. Pseudocounts added to avoid NAs
MutualInfCompute Information Coefficient [IC] Pablo Tamayo Dec 30,...
nnsvd_initNonnegative SVD initialization
NormalizeCountsNormalization and batch effect removal adapted from pagoda2...
normalize_vectorHelper function for normalizing vectors with different...
PlotDimsPlots 2D embedding
PlotFactorSelectionPlot decrease in reconstruction error versus random noise....
PlotSWNEPlots swne embedding
PlotSWNEVelocytoPlots swne embedding with RNA velocity arrows overlaid
ProjectFeaturesProjects new features onto existing factor decomposition
ProjectGenesetsProjects dataset onto genesets using either NMF or a...
ProjectSamplesProjects new samples onto existing factor decomposition
ProjectSNNCalculates shared nearest neighbors between samples (columns)...
ProjectSWNEProjects new data onto an existing swne embedding
ReadDataReads data from a sparse or dense matrix Adapted from Seurat
ReadGenesetsLoad genesets from gmt file. For more info on the .gmt file...
ReadGroupsRead in sample groups from a csv file format
RenameFactorsFunction for renaming NMF factors to something more...
RunGSEARuns GSEA on the gene association coefficients for each NMF
RunNMFRuns NMF decomposition on a data matrix: A = WH.
RunSWNEWrapper for the running SWNE analysis functions
ScaleCountsNormalize, adjust feature variance, and scale data matrix
SelectFeaturesSelect overdispersed features
SelectGenesetsSelect genesets for embedding
SummarizeAssocFeaturesSummarize the factors x features association matrix into a...
UnflattenDataframeConvert dataframe to matrix, specifying all column names
UnflattenGroupsConverts a flat sample groups character vector into a list...
VelocytoArrowsFunction for computing arrows to add onto a ggplot2 object....
winsorize_matrixInternal function for winsorizing a matrix Adapted from...
WriteGenesetsWrites genesets to gmt file
WriteGroupsWrite sample groups from list to csv format
yanwu2014/swne documentation built on Oct. 4, 2018, 10:17 p.m.