lfranzen / scwat-st Goto Github PK

Error in file(file, ifelse(append, "a", "w")) : cannot open the connection
6.
file(file, ifelse(append, "a", "w"))
5.
write.table(c_anno, file = file.path(DIR_RES, "tables", fname), row.names = F, col.names = TRUE, sep = ",", dec = ".", qmethod = "double")
4.
eval(expr, p)
3.
eval(expr, p)
2.
eval.parent(Call)
1.
write.csv(c_anno, file = file.path(DIR_RES, "tables", fname), row.names = F)

Error in open.connection(con, "rb") : cannot open the connection
12.
open.connection(con, "rb")
11.
open(con, "rb")
10.
parse_con(txt, bigint_as_char)
9.
parseJSON(txt, bigint_as_char)
8.
parse_and_simplify(json, simplifyVector = simplifyVector, ...)
7.
parse_json(file(path), simplifyVector = simplifyVector, ...)
6.
read_json(f)
5.
FUN(X[[i]], ...)
4.
lapply(X = X, FUN = FUN, ...)
3.
sapply(infotable[, "json"], function(f) { read_json(f)$tissue_hires_scalef })
2.
scaleVisium %||% sapply(infotable[, "json"], function(f) { read_json(f)$tissue_hires_scalef })
1.
InputFromTable(infotable = infoTable, min.gene.count = 100, min.gene.spots = 5, min.spot.count = 200, platform = "Visium")

#' Read in original se object in case minor random changes in the SCTransform/ICA/UMAP has occurred
se <- readRDS(file = file.path(DIR_DATA, "se-object.visium_baseline_ori.rds"))
se@tools$Staffli@imgs <- infoTable$imgs

Error in gzfile(file, "rb") : cannot open the connection
2.
gzfile(file, "rb")
1.
readRDS(file = file.path(DIR_DATA, "se-object.visium_baseline_ori.rds"))