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