Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

AdjustVariance | Adjust feature variance to remove effect of varying feature... |

CalcGenesetLoadings | Calculate geneset factor loadings from gene factor loadings |

CalcSNN | SNN Graph Construction. Adapted from Seurat. |

CheckGeneEmbedding | Validates gene embeddings by plotting cluster logFC vs gene... |

clean_genesets | Helper function for filtering genesets |

ClusterIndicatorMatrix | Creates a clusters x cells indicator matrix where a 1 means... |

compute_projected_snn | Helper function for calculating a SNN graph Adapted from... |

EmbedContours | Embeds data for generating elliptical contours to mark areas... |

EmbedFeatures | Embeds features relative to factor coordinates |

EmbedGenesets | Embeds genesets relative to factor coordinates |

EmbedSWNE | Embeds NMF factors and samples in 2 dimensions |

ExtractDebatchedSeurat | Reconstructs the gene expression matrix from the CCA gene... |

ExtractField | Extract a field from a delimited string |

ExtractNormCounts | Extracts scaled counts from Seurat or Pagoda2 objects |

ExtractSWNEColors | Extracts the exact colors used to plot each cluster (the hex... |

FactorAssociation | Find the top gene or geneset markers for each NMF factor... |

FeaturePlotDims | Plots 2d embedding with feature overlayed |

FeaturePlotSWNE | Plots swne embedding with feature overlayed |

FilterData | Filter data by minimum cells, minimum genes, and winsorizes... |

FilterGenesets | Filters genesets according to minimum and maximum set size |

FindNumFactors | Determines the optimal number of NMF factors to use by... |

FlattenGroups | Convert list of sample groups into a flat vector. Removes all... |

ft_transform | Freeman-Tukey transform for variance stabilization |

genesets_indicator | Creates a genes x genesets indicator matrix |

get_factor_coords | Calculates the coordinates of the NMF factors via Sammon... |

get_sample_coords | Calculate sample coordinates using the NMF scores and NMF... |

ggHeat | Plots a heatmap using ggplot2 |

ica_init | Independent component analysis initialization. Negative... |

kl_div | KL divergence. Pseudocounts added to avoid NAs |

MutualInf | Compute Information Coefficient [IC] Pablo Tamayo Dec 30,... |

nnsvd_init | Nonnegative SVD initialization |

NormalizeCounts | Normalization and batch effect removal adapted from pagoda2... |

normalize_vector | Helper function for normalizing vectors with different... |

PlotDims | Plots 2D embedding |

PlotFactorSelection | Plot decrease in reconstruction error versus random noise.... |

PlotSWNE | Plots swne embedding |

ProjectFeatures | Projects new features onto existing factor decomposition |

ProjectGenesets | Projects dataset onto genesets using either NMF or a... |

ProjectSamples | Projects new samples onto existing factor decomposition |

ProjectSNN | Calculates shared nearest neighbors between samples (columns)... |

ProjectSWNE | Projects new data onto an existing swne embedding |

ReadData | Reads data from a sparse or dense matrix Adapted from Seurat |

ReadGenesets | Load genesets from gmt file. For more info on the .gmt file... |

ReadGroups | Read in sample groups from a csv file format |

RenameFactors | Function for renaming NMF factors to something more... |

RunGSEA | Runs GSEA on the gene association coefficients for each NMF |

RunNMF | Runs NMF decomposition on a data matrix: A = WH. |

RunSWNE | Wrapper for running SWNE analysis |

ScaleCounts | Normalize, adjust feature variance, and scale data matrix |

SelectFeatures | Select overdispersed features |

SelectGenesets | Select genesets for embedding |

SummarizeAssocFeatures | Summarize the factors x features association matrix into a... |

UnflattenDataframe | Convert dataframe to matrix, specifying all column names |

UnflattenGroups | Converts a flat sample groups character vector into a list... |

winsorize_matrix | Internal function for winsorizing a matrix Adapted from... |

WriteGenesets | Writes genesets to gmt file |

WriteGroups | Write sample groups from list to csv format |

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