Create spatial vectors for genes from transcript coordinates
Source:R/get_vectors.R
get_gene_vectors_tr.Rd
This function will build gene vectors based on the transcript coordinates of every gene
Arguments
- trans_lst
If specified, it is a list of named dataframes. Each dataframe refers to one sample and shows the transcript detection coordinates for each gene. Optional parameter.
- all_genes
A vector of strings giving the name of the genes you want to test. This will be used as column names for one of the result matrix
gene_mt
.- bin_type
A string indicating which bin shape is to be used for vectorization. One of "square" (default), "rectangle", or "hexagon".
- bin_param
A numeric vector indicating the size of the bin. If the
bin_type
is "square" or "rectangle", this will be a vector of length two giving the numbers of rectangular quadrats in the x and y directions. If thebin_type
is "hexagonal", this will be a number giving the side length of hexagons. Positive numbers only.- bin_length
A positive integer giving the length of total bins
- w_x
A numeric vector of length two specifying the x coordinate limits of enclosing box.
- w_y
A numeric vector of length two specifying the y coordinate limits of enclosing box.