On Aug 8, 2014, at 11:28 AM, Fix Ace wrote:
> I recently tried to run some sample code from R package: circlize,
> and got an error message (please see below) ===== > library(circlize) >
> circos.genomicInitialize(df) > df = data.frame(name = c("TP53", "TP63",
> "TP73"), + start = c(7565097, 189349205, 3569084),
> + end = c(7590856, 189615068, 3652765),
> + stringsAsFactors = FALSE) > df name start end
> 1 TP53 7565097 7590856
> 2 TP63 189349205 189615068
> 3 TP73 3569084 3652765 > circos.genomicInitialize(df) > circos.clear() >
> circos.genomicInitialize(df, major.by = 10000) Error in seq.default(xlim[1],
> 10^nchar(round(max(x2 - x1 + 1))), by =
> major.by) : wrong sign in 'by' argument === And my session information: >
> sessionInfo() R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8
> LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=C [5]
> LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8
> LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages:
> [1] stats graphics grDevices utils datasets methods base other
> attached packages:
> [1] circlize_0.1.0 loaded via a namespace (and not attached): [1]
> AnnotationDbi_1.26.0 Biobase_2.24.0 BiocGenerics_0.10.0 [4]
> DBI_0.2-7 DESeq2_1.4.5 GenomeInfoDb_1.0.2 [7]
> GenomicRanges_1.16.3 IRanges_1.22.9 RColorBrewer_1.0-5
> [10] RSQLite_0.11.4 Rcpp_0.11.2 RcppArmadillo_0.4.320.0
> [13] XML_3.98-1.1 XVector_0.4.0 annotate_1.42.1
> [16] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.1
> [19] lattice_0.20-29 locfit_1.5-9.1 parallel_3.1.1
> [22] splines_3.1.1 stats4_3.1.1 survival_2.37-7
> [25] xtable_1.7-3 > ===
>
> Wonder anyone could please help me out with this?
>
> Thank you very much for your time.:)
>
> [[alternative HTML version deleted]]
Your failure to post in plain text makes this message very difficult to read.
Unless there is someone with more patience than I have who responds in the next
12 hours, you might consider reposting after reading the Posing Guide.
--
David Winsemius
Alameda, CA, USA
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