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[Pruning] Fusions patch and csv export in pgv function #120

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[Pruning] Fusions patch and csv export in pgv function #120

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8e5e647
Fusions patch and csv export in pgv function
DoaneAS May 18, 2022
49397a1
Merge pull request #90 from DoaneAS/dev
shihabdider Oct 10, 2023
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2 changes: 1 addition & 1 deletion R/gGnome.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3908,7 +3908,7 @@ gGraph = R6::R6Class("gGraph",
## convert to integer .. and back to snode.id
## if path does not exist get.shortest.paths (for some reason) will return a single vector with the target
## so we clean out all paths that don't have the query
v = lapply(p$vpath, function(x) {y = as.integer(x); if (length(y) == 0 | is.na(y[1]) | y[1] != query) return(c()) else return(snode.id[y])})
v = lapply(p$vpath, function(x) {y = as.integer(x); if (length(y) == 0 || is.na(y[1]) || y[1] != query) return(c()) else return(snode.id[y])})
## chop off the last interval to get the "true" distance from query to subject
if (do.trim)
{
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18 changes: 14 additions & 4 deletions R/jsUtils.R
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Expand Up @@ -684,7 +684,7 @@ is.acceptable.js.type = function(js.type){
#' @export
gen_js_coverage_files = function(data, outdir, name.col = 'sample', overwrite = FALSE, cov.col = 'coverage',
js.type = 'gGnome.js', cov.field = 'ratio', cov.field.col = NA,
bin.width = 1e4, dataset_name = NA, ref = 'hg19', gg.col = 'graph',
bin.width = 1e4, dataset_name = NA, ref = 'hg38', gg.col = 'graph',
cov.color.field = NULL, meta.js = NULL, kag.col = kag.col,
ncn.gr = ncn.gr, mc.cores = 1){
if (!is.na(cov.field.col)){
Expand Down Expand Up @@ -1082,7 +1082,7 @@ cov2csv = function(cov,
cov2arrow = function(cov,
field = "ratio",
output_file = 'coverage.arrow',
ref = 'hg19',
ref = 'hg38_chr',
cov.color.field = NULL,
overwrite = FALSE,
meta.js = NULL,
Expand Down Expand Up @@ -1126,8 +1126,18 @@ cov2arrow = function(cov,
outdt = outdt[order(x)]

message('Writing arrow file (using write_feather)')
arrow_table = arrow::Table$create(outdt, schema = arrow::schema(x = arrow::float32(), y = arrow::float32(), color = arrow::float32()))
arrow::write_feather(arrow_table, output_file)
#arrow_table = arrow::Table$create(outdt, schema = arrow::schema(x = arrow::float64(), y = arrow::float64(), color = arrow::float64()))
#arrow::write_feather(arrow_table, output_file)

arrow::write_feather(outdt, output_file)


message('Writing csv file')
#arrow_table = arrow::Table$create(outdt, schema = arrow::schema(x = arrow::float64(), y = arrow::float64(), color = arrow::float64()))
#arrow::write_feather(arrow_table, output_file)
output_csv = stringr::str_replace(output_file, "arrow", "csv")
data.table::fwrite(outdt, output_csv, sep=",")

} else {
message('arrow file, "', output_file, '" already exists.')
}
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