Convert the coordinates of set of genes into vectors.
Source:R/create_genesets.R
create_genesets.Rd
Convert the coordinates of set of genes into vectors.
Usage
create_genesets(
data_lst,
name_lst,
bin_type = "square",
bin_param,
w_x = w_x,
w_y = w_y,
cluster_info
)
Arguments
- data_lst
A list of named matrices containing the coordinates of transcripts.
- name_lst
A named list of strings giving the name of features that are treated as background.
- 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.- 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.
- cluster_info
A dataframe/matrix containing the centroid coordinates, cluster and sample label for each cell.The column names must include "x" (x coordinate), "y" (y coordinate), "cluster" (cluster label) and "sample" (sample).
Value
A matrix contains the sum count in each grid.
Each row refers to a grid, each column refers to a set in name_lst
.
The column name will match the names in name_lst
.
Examples
set.seed(15)
trans = as.data.frame(rbind(cbind(x = runif(10, min=1, max=10),
y = runif(10, min=1, max=10),
feature_name="A"),
cbind(x = runif(5, min=10, max=24),
y = runif(5, min=1, max=10),
feature_name="B"),
cbind(x = runif(10, min=10, max=24),
y = runif(10, min=10, max=24),
feature_name="C")))
trans$x = as.numeric(trans$x)
trans$y = as.numeric(trans$y)
geneset_res = create_genesets(data_lst=list("rep1"= trans),
name_lst=list(dummy_A=c("A","C"),
dummy_B=c("A","B","C")),
bin_type="square",
bin_param=c(2,2),
w_x=c(0,25), w_y=c(0,25), cluster_info=NULL)