error in htmlwidges

[Estherrr1997]

Hi there,

I have installed Dotplotly and I try to run it using my data but I get this error (the same error occurs when
running dotplotly on the example data):

admin_bi@GSYMK2:/media/admin_bi/DATA/Files_Esther/dotPlotly$ ./pafCoordsDotPlotly.R -i /media/admin_bi/DATA/Files_Esther/paf_files/blue_shark_white_shark.paf -o out -s -t -m 500 -q 500000 -k 7 -l
PARAMETERS:
input (-i): /media/admin_bi/DATA/Files_Esther/paf_files/blue_shark_white_shark.paf
output (-o): out
minimum query aggregate alignment length (-q): 5e+05
minimum alignment length (-m): 500
plot size (-p): 15
show horizontal lines (-l): TRUE
number of reference chromosomes to keep (-k): 7
show % identity (-s): TRUE
show % identity for on-target alignments only (-t): TRUE
produce interactive plot (-x): TRUE
reference IDs to keep (-r):

Number of alignments: 139943
Number of query sequences: 567

After filtering... Number of alignments: 6919
After filtering... Number of query sequences: 6

Error in htmlwidgets::saveWidget(as.widget(gply), file = paste0(opt$output_filename, :
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
No traceback available

When running only the R script, I get this message:
admin_bi@GSYMK2:/media/admin_bi/DATA/Files_Esther/dotPlotly$ ./pafCoordsDotPlotly.R
PARAMETERS:
input (-i):
output (-o): out
minimum query aggregate alignment length (-q): 4e+05
minimum alignment length (-m): 10000
plot size (-p): 15
show horizontal lines (-l): FALSE
number of reference chromosomes to keep (-k):
show % identity (-s): FALSE
show % identity for on-target alignments only (-t): FALSE
produce interactive plot (-x): TRUE
reference IDs to keep (-r):
Error in read.table(opt$input_filename, stringsAsFactors = F, fill = T) :
'file' must be a character string or connection
No traceback available
Error in colnames(alignments)[1:12] = c("queryID", "queryLen", "queryStart", :
object 'alignments' not found
2: stop("'file' must be a character string or connection")
1: read.table(opt$input_filename, stringsAsFactors = F, fill = T)
Error: object 'alignments' not found
No traceback available
Error: object 'alignments' not found
No traceback available
Error: object 'alignments' not found
No traceback available
Error: object 'queryStartTemp' not found
No traceback available
Warning message:
In rm(queryStartTemp) : object 'queryStartTemp' not found
Error in nrow(alignments) : object 'alignments' not found
Calls: cat -> paste0 -> nrow
No traceback available
Error in unique(alignments$queryID) : object 'alignments' not found
Calls: cat -> paste0 -> unique
3: nrow(alignments)
2: paste0("\nNumber of alignments: ", nrow(alignments), "\n")
1: cat(paste0("\nNumber of alignments: ", nrow(alignments), "\n"))
Error in tapply(alignments$refEnd, alignments$refID, max) :
object 'alignments' not found
3: unique(alignments$queryID)
2: paste0("Number of query sequences: ", length(unique(alignments$queryID)),
"\n")
1: cat(paste0("Number of query sequences: ", length(unique(alignments$queryID)),
"\n"))
Error in tapply(alignments$lenAln, alignments$queryID, sum) :
object 'alignments' not found
1: tapply(alignments$refEnd, alignments$refID, max)
Error: object 'alignments' not found
1: tapply(alignments$lenAln, alignments$queryID, sum)
Error: object 'alignments' not found
No traceback available
Error in tapply(alignments$lenAln, alignments$queryID, sum) :
object 'alignments' not found
No traceback available
Error: object 'alignments' not found
1: tapply(alignments$lenAln, alignments$queryID, sum)
Error in nrow(alignments) : object 'alignments' not found
Calls: cat -> paste0 -> nrow
No traceback available
Error in unique(alignments$queryID) : object 'alignments' not found
Calls: cat -> paste0 -> unique
3: nrow(alignments)
2: paste0("\nAfter filtering... Number of alignments: ", nrow(alignments),
"\n")
1: cat(paste0("\nAfter filtering... Number of alignments: ", nrow(alignments),
"\n"))
Error in factor(alignments$refID, levels = refIDsToKeepOrdered) :
object 'alignments' not found
3: unique(alignments$queryID)
2: paste0("After filtering... Number of query sequences: ", length(unique(alignments$queryID)),
"\n\n")
1: cat(paste0("After filtering... Number of query sequences: ",
length(unique(alignments$queryID)), "\n\n"))
Error: object 'alignments' not found
1: factor(alignments$refID, levels = refIDsToKeepOrdered)
Error in tapply(alignments$refEnd, alignments$refID, max) :
object 'alignments' not found
No traceback available
Error in levels(alignments$refID) : object 'alignments' not found
1: tapply(alignments$refEnd, alignments$refID, max)
Error in factor(alignments$queryID, levels = unique(as.character(alignments$queryID))) :
object 'alignments' not found
1: levels(alignments$refID)
Error in tapply(alignments$lenAln, alignments$queryID, which.max, simplify = F) :
object 'alignments' not found
1: factor(alignments$queryID, levels = unique(as.character(alignments$queryID)))
Error in factor(alignments$queryID, levels = unique(as.character(alignments$queryID))[order(mapply(function(x, :
object 'alignments' not found
1: tapply(alignments$lenAln, alignments$queryID, which.max, simplify = F)
Error in levels(alignments$queryID) : object 'alignments' not found
Calls: sapply -> lapply -> levels
1: factor(alignments$queryID, levels = unique(as.character(alignments$queryID))[order(mapply(function(x,
i) alignments$refStart2[which(i == alignments$queryID)][x],
queryMaxAlnIndex, names(queryMaxAlnIndex)))])
Error in levels(alignments$refID) : object 'alignments' not found
3: levels(alignments$queryID)
2: lapply(X = X, FUN = FUN, ...)
1: sapply((levels(alignments$queryID)), function(x) tapply(alignments$lenAln[which(alignments$queryID ==
x)], alignments$refID[which(alignments$queryID == x)], sum))
Error in factor(alignments$queryID, levels = (levels(alignments$queryID))[order(match(queryID_Ref, :
object 'alignments' not found
1: levels(alignments$refID)
Error in tapply(alignments$queryEnd - alignments$queryStart, alignments$queryID, :
object 'alignments' not found
1: factor(alignments$queryID, levels = (levels(alignments$queryID))[order(match(queryID_Ref,
levels(alignments$refID)))])
Error: object 'queryRevComp' not found
1: tapply(alignments$queryEnd - alignments$queryStart, alignments$queryID,
function(x) sum(x))
Error in tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID, :
object 'alignments' not found
No traceback available
Error in levels(alignments$queryID) : object 'alignments' not found
1: tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID,
alignments$queryID), max)
Error: object 'queryMax' not found
1: levels(alignments$queryID)
Error: object 'queryMax' not found
No traceback available
Error in tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID, :
object 'alignments' not found
No traceback available
Error in levels(alignments$queryID) : object 'alignments' not found
1: tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID,
alignments$queryID), min)
Error: object 'alignments' not found
1: levels(alignments$queryID)
Error: object 'alignments' not found
No traceback available
Error in tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID, :
object 'alignments' not found
No traceback available
Error in levels(alignments$queryID) : object 'alignments' not found
1: tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID,
alignments$queryID), max)
Error: object 'alignments' not found
1: levels(alignments$queryID)
Error: object 'alignments' not found
No traceback available
Error in levels(alignments$refID) : object 'alignments' not found
No traceback available
Error in tapply(alignments$queryEnd2, alignments$queryID, max) :
object 'alignments' not found
1: levels(alignments$refID)
Error in ggplot(alignments) : object 'alignments' not found
1: tapply(alignments$queryEnd2, alignments$queryID, max)
Error in ggplotly(gp, tooltip = "text") : object 'gp' not found
1: ggplot(alignments)

What happens here and how can I solve this?

Kind regards,
Esther