Man pages for yanwu2014/swne
Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets
| AdjustVariance | Adjust feature variance to remove effect of varying feature... |
| BuildPAGA | Make PAGA graph. Adapted from Monocle3 |
| CalcGenesetLoadings | Calculate geneset factor loadings from gene factor loadings |
| CalcKNN | kNN Graph Construction. Adapted from Seurat. |
| 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_partitions | Compute significant links between specified clusters Adapted... |
| compute_projected_snn | Helper function for calculating a SNN graph Adapted from... |
| EmbedFeatures | Embeds features relative to factor coordinates |
| EmbedPromoters | Embeds genes based on promoter accessibility relative to... |
| EmbedSWNE | Embeds NMF factors and samples in 2 dimensions |
| EmbedTFBS | Embeds genes based on TF binding site accessibility relative... |
| 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... |
| ggBarplot | Make simple barplot from vector |
| 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... |
| PartitionSimilarityGraph | Create a graph of cosine similarities between clusters pruned... |
| 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 |
| PruneSNN | Prune SNN with PAGA graph. Adapted from Monocle3 |
| Read10XHuman | Reads a 10X matrix aligned to a mouse/human reference and... |
| 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 |
