parseSpotFile: Parse spot detector output

In SpatialCPie: Cluster analysis of Spatial Transcriptomics data

Description

Parses the output from the ST spot detector tool for use with SpatialCPie.

Usage

parseSpotFile(file)

Arguments

file

spot file

Value

data.frame with columns "x" and "y" specifying the pixel coordinates of each spot

Examples

## Create spot file
data <- rbind(
    c(7, 18, 7.00, 18.07, 563.2, 947.0),
    c(8, 11, 8.00, 11.04, 612.5, 627.7)
)
filename <- tempfile()
write.table(
    data,
    file = filename,
    sep = "\t",
    quote = FALSE,
    col.names = c("x", "y", "new_x", "new_y", "pixel_x", "pixel_y")
)

## Parse spot file
parseSpotFile(filename)

## Delete spot file
unlink(filename)

Example output

Warning message:
In grepl("^[a-z0-9\\-_][a-z0-9\\-_.]*$", prefix, ignore.case = TRUE,  :
  PCRE JIT compilation error
	'no more memory'
         x     y
7x18 563.2 947.0
8x11 612.5 627.7
Warning message:
system call failed: Cannot allocate memory 

SpatialCPie documentation built on Nov. 8, 2020, 7:43 p.m.