+ -src.embed module# +src.embed module# -Command line interface# +Command line interface# -pathogen-embed# +pathogen-embed# Reduced dimension embeddings for pathogen sequences -usage: pathogen-embed [-h] --alignment ALIGNMENT [--distance-matrix DISTANCE_MATRIX] [--separator SEPARATOR] - [--indel-distance] [--random-seed RANDOM_SEED] [--output-dataframe OUTPUT_DATAFRAME] - [--output-figure OUTPUT_FIGURE] [--embedding-parameters EMBEDDING_PARAMETERS] +usage: pathogen-embed [-h] --alignment ALIGNMENT [ALIGNMENT ...] [--distance-matrix DISTANCE_MATRIX [DISTANCE_MATRIX ...]] [--separator SEPARATOR] [--indel-distance] + [--random-seed RANDOM_SEED] [--output-dataframe OUTPUT_DATAFRAME] [--output-figure OUTPUT_FIGURE] [--embedding-parameters EMBEDDING_PARAMETERS] + [--output-pairwise-distance-figure OUTPUT_PAIRWISE_DISTANCE_FIGURE] {pca,t-sne,umap,mds} ... -Positional Arguments# +Positional Arguments# command Possible choices: pca, t-sne, umap, mds @@ -475,13 +361,13 @@ Positional Arguments -Named Arguments# +Named Arguments# --alignment -an aligned FASTA file to create a distance matrix with. Make sure the strain order in this file matches the order in the distance matrix. +an aligned FASTA file (or files) to create a distance matrix with. Make sure the strain order in this file matches the order in the distance matrix. If adding more than one alignment, make sure the order of the strains and strain names are the same between all the files. --distance-matrix -a distance matrix that can be read in by pandas, index column as row 0 +a distance matrix (or matrices) that can be read in by pandas, index column as row 0. If adding more than one distance matrix, make sure the order of the strains and strain names in the header are the same between all the files. --separator separator between columns in the given distance matrix @@ -499,23 +385,26 @@ Named Arguments -Sub-commands# +Sub-commands# -pca# +pca# Principal Component Analysis pathogen-embed pca [-h] [--components COMPONENTS] [--explained-variance EXPLAINED_VARIANCE] -Named Arguments# +Named Arguments# --components the number of components for PCA @@ -528,13 +417,13 @@ Named Arguments -t-sne# +t-sne# t-distributed Stochastic Neighborhood Embedding pathogen-embed t-sne [-h] [--components COMPONENTS] [--perplexity PERPLEXITY] [--learning-rate LEARNING_RATE] -Named Arguments# +Named Arguments# --components the number of components for t-SNE @@ -546,26 +435,26 @@ Named Arguments -umap# +umap# Uniform Manifold Approximation and Projection pathogen-embed umap [-h] [--components COMPONENTS] [--nearest-neighbors NEAREST_NEIGHBORS] [--min-dist MIN_DIST] -Named Arguments# +Named Arguments# --components the number of components for UMAP Default: 2 --nearest-neighbors -Nearest neighbors controls how UMAP balances local versus global structure in the data (finer detail patterns versus global structure). This value is proportional to the size of the data (large dataset -> large nearest neighbors. The default value is the value consistently the best for pathogen analyses, results from an exhaustive grid search. +Nearest neighbors controls how UMAP balances local versus global structure in the data (finer detail patterns versus global structure). This value is proportional to the size of the data (large dataset -> large nearest neighbors). The default value is the value consistently the best for pathogen analyses, results from an exhaustive grid search. Default: 200 --min-dist @@ -576,32 +465,35 @@ Named Arguments -mds# +mds# Multidimensional Scaling -pathogen-embed mds [-h] [--components COMPONENTS] +pathogen-embed mds [-h] [--components COMPONENTS] [--stress STRESS] -Named Arguments# +Named Arguments# --components the number of components for MDS Default: 10 +--stress +the path for the CSV stress for the embedding + -pathogen-distance# +pathogen-distance# Hamming distance (optionally indel sensitive) similarity matrix for pathogen sequences usage: pathogen-distance [-h] --alignment ALIGNMENT [--indel-distance] --output OUTPUT -Named Arguments# +Named Arguments# --alignment an aligned FASTA file to create a distance matrix with. Make sure the strain order in this file matches the order in the distance matrix. @@ -617,16 +509,15 @@ Named Arguments -pathogen-cluster# +pathogen-cluster# HDBSCAN clustering for reduced dimension embeddings -usage: pathogen-cluster [-h] --embedding EMBEDDING [--label-attribute LABEL_ATTRIBUTE] [--random-seed RANDOM_SEED] - [--min-size MIN_SIZE] [--min-samples MIN_SAMPLES] [--distance-threshold DISTANCE_THRESHOLD] - --output-dataframe OUTPUT_DATAFRAME [--output-figure OUTPUT_FIGURE] +usage: pathogen-cluster [-h] --embedding EMBEDDING [--label-attribute LABEL_ATTRIBUTE] [--random-seed RANDOM_SEED] [--min-size MIN_SIZE] [--min-samples MIN_SAMPLES] + [--distance-threshold DISTANCE_THRESHOLD] --output-dataframe OUTPUT_DATAFRAME [--output-figure OUTPUT_FIGURE] -Named Arguments# +Named Arguments# --embedding The embedding to assign clustering labels to via HDBSCAN (https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html) @@ -659,43 +550,125 @@ Named Arguments -API# +API# pathogen-embed. Reduced dimension embeddings for pathogen sequences. - + - - - + + + + + + + + + Contents + + + +Command line interface +pathogen-embed +Positional Arguments +Named Arguments +Sub-commands +pca +Named Arguments + + +t-sne +Named Arguments + + +umap +Named Arguments + + +mds +Named Arguments + + + + + + +pathogen-distance +Named Arguments + + +pathogen-cluster +Named Arguments + + +API + + + + + + + + + + + + + + + + + + +