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#
# plot of genome data such as fusion and variant
#
# You can learn more about package authoring with RStudio at:
#
# http://r-pkgs.had.co.nz/
#
# Some useful keyboard shortcuts for package authoring:
#
# Build and Reload Package: 'Cmd + Shift + B'
# Check Package: 'Cmd + Shift + E'
# Test Package: 'Cmd + Shift + T'
gvmap <- function(data_file, config_file, output_svg_name) {
# check output parameter
if (file.exists(output_svg_name)) {
message("** ", output_svg_name , " already exists, the gvmap result will replace it.")
}
# read file
data_info <- readDataFile(data_file)
config_info <- readConfig(config_file)
map_config <- config_info$map_config
color_config <- config_info$color_config
rect_config <- config_info$rect_config
# plot sample name
sample_svg <- getSampleEle(data_info, map_config, color_config, rect_config)
# plot group information
group_svg <- lapply(1:map_config$group_num, function(i) {
plotGroup(data_info, map_config, color_config, rect_config, i)
})
group_svg <- paste(group_svg, collapse = "\n")
# add location
loc_svg <- addLoc(map_config, rect_config)
# output svg file
output_info <- list(
sample_svg = sample_svg,
group_svg = group_svg,
loc_svg = loc_svg
)
outputSVG(output_info, output_svg_name, rect_config)
}
# output SVG result
outputSVG <- function(output_info, output_svg_name, rect_config) {
write(SVGheader(rect_config$plot_width, rect_config$plot_height), file = output_svg_name, sep = "\n")
write(SVGdefHeader(), file = output_svg_name, append = T, sep = "\n")
write(output_info$sample_svg, file = output_svg_name, append = T, sep = "\n")
write(output_info$group_svg, file = output_svg_name, append = T, sep = "\n")
write(SVGdefFooter(), file = output_svg_name, append = T, sep = "\n")
write(output_info$loc_svg, file = output_svg_name, append = T, sep = "\n")
write(SVGfooter(), file = output_svg_name, append = T, sep = "\n")
}
# read data file
readDataFile <- function(data_file) {
if (typeof(data_file) == "character") {
data_info <- read.table(data_file, header = T, sep = "\t", quote = '"')
} else {
data_info <- data_file
}
return(data_info)
}
# read map config file
readConfig <- function(config_file) {
if (is.yaml.file(config_file)) {
config_info <- read.config(config_file)
} else {
stop("must input a right config file of YAML format")
}
return(config_info)
}
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