Function reference • singleCellHaystack

Main haystack functions
`haystack()`	The main Haystack function
`haystack_2D()`	The main Haystack function, for 2-dimensional spaces.
`haystack_highD()`	The main Haystack function, for higher-dimensional spaces.
`haystack_continuous_highD()`	The main Haystack function, for higher-dimensional spaces and continuous expression levels.
`show_result_haystack()`	show_result_haystack
Visualization functions
`plot_gene_haystack()`	Visualizing the detection/expression of a gene in a 2D plot
`plot_gene_haystack_raw()`	Visualizing the detection/expression of a gene in a 2D plot
`plot_gene_set_haystack()`	Visualizing the detection/expression of a set of genes in a 2D plot
`plot_gene_set_haystack_raw()`	Visualizing the detection/expression of a set of genes in a 2D plot
`plot_rand_fit()`	plot_rand_fit
Clustering functions
`hclust_haystack()`	Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space
`hclust_haystack_highD()`	Function for hierarchical clustering of genes according to their distribution in a higher-dimensional space.
`hclust_haystack_raw()`	Function for hierarchical clustering of genes according to their distribution on a 2D plot.
`kmeans_haystack()`	Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space
`kmeans_haystack_highD()`	Function for k-means clustering of genes according to their distribution in a higher-dimensional space.
`kmeans_haystack_raw()`	Function for k-means clustering of genes according to their distribution on a 2D plot.
IO functions
`read_haystack()`	Function to read haystack results from file.
`write_haystack()`	Function to write haystack result data to file.
Toy example data
`dat.expression`	Single cell RNA-seq dataset.
`dat.tsne`	Single cell tSNE coordingates.
Background functions
`default_bandwidth.nrd()`	Default function given by function bandwidth.nrd in MASS. No changes were made to this function.
`extract_row_dgRMatrix()`	Returns a row of a sparse matrix of class dgRMatrix. Function made by Ben Bolker and Ott Toomet (see https://stackoverflow.com/questions/47997184/)
`extract_row_lgRMatrix()`	Returns a row of a sparse matrix of class lgRMatrix. Function made by Ben Bolker and Ott Toomet (see https://stackoverflow.com/questions/47997184/)
`get_D_KL()`	Calculates the Kullback-Leibler divergence between distributions.
`get_D_KL_highD()`	Calculates the Kullback-Leibler divergence between distributions for the high-dimensional version of haystack().
`get_D_KL_continuous_highD()`	Calculates the Kullback-Leibler divergence between distributions for the high-dimensional continuous version of haystack.
`get_density()`	Function to get the density of points with value TRUE in the (x,y) plot
`get_dist_two_sets()`	Calculate the pairwise Euclidean distances between the rows of 2 matrices.
`get_euclidean_distance()`	Calculate the Euclidean distance between x and y.
`get_grid_points()`	A function to decide grid points in a higher-dimensional space
`get_log_p_D_KL()`	Estimates the significance of the observed Kullback-Leibler divergence by comparing to randomizations.
`get_log_p_D_KL_continuous()`	Estimates the significance of the observed Kullback-Leibler divergence by comparing to randomizations for the continuous version of haystack.
`get_parameters_haystack()`	Function that decides most of the parameters that will be used during the "Haystack" analysis.
`get_reference()`	Get reference distribution
`kde2d_faster()`	Based on the MASS kde2d() function, but heavily simplified; it's just tcrossprod() now.
Development
`plot_compare_ranks()`	plot_compare_ranks
`plot_rand_KLD()`	plot_rand_KLD

Reference

Main haystack functions

Visualization functions

Clustering functions

IO functions

Toy example data

Background functions

Development