Dear Jianqiang, I am cc'ing the list - maybe somebody else will have the same issue. You are correct, qQCReport() was altering the default color palette. This is fixed now in versions 1.2.2 (release) and 1.3.5 (development) and should become available in a day or two from now. As a quick workaround, you can get back the default palette by calling: palette("default") this will set the numberical color values to be taken from: c("black","red","green3","blue","cyan","magenta","yellow","gray") Best wishes, Michael On 09.11.2013 02:55, SUN jianqiang wrote: > Dear Michael, > > > Hi, thank you for your convenient package. > > I have a question about QuasR::qQCReport. > I have found the reason about the question. > However, I could not find that. > Could you help me? > > If I run following command, I can got the figure such as Fig1.png on > attachment. > >> plot(1:10,col=c(1:10),pch=20,cex=5) > > However, after execute qQCReport, the default colors have been changed. > Such as Fig2.png. > >> qQCReport(qAline.result, pdfFilename="test.pdf") >> plot(1:10,col=c(1:10),pch=20,cex=5) > > > Could you tell me how to restore the default colors after running > qQCReport? > > > Thank you. > > > Jianqiang, SUN > > > > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] RUnit_0.4.26 BSgenome.Hsapiens.UCSC.hg19_1.3.19 > [3] BSgenome_1.30.0 Biostrings_2.30.0 > [5] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 > [7] Biobase_2.22.0 QuasR_1.2.1 > [9] Rbowtie_1.2.0 GenomicRanges_1.14.3 > [11] XVector_0.2.0 IRanges_1.20.5 > [13] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 baySeq_1.16.0 BiocInstaller_1.12.0 > [4] biomaRt_2.18.0 bitops_1.0-6 DBI_0.2-7 > [7] DESeq_1.14.0 EBSeq_1.2.0 edgeR_3.4.0 > [10] genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 > [13] hwriter_1.3 lattice_0.20-24 latticeExtra_0.6-26 > [16] limma_3.18.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [19] ROC_1.38.0 Rsamtools_1.14.1 RSQLite_0.11.4 > [22] rtracklayer_1.22.0 samr_2.0 ShortRead_1.20.0 > [25] splines_3.0.2 stats4_3.0.2 survival_2.37-4 > [28] TCC_1.2.0 tools_3.0.2 XML_3.98-1.1 > [31] xtable_1.7-1 zlibbioc_1.8.0 > > -- -------------------------------------------- Michael Stadler, PhD Head of Computational Biology Friedrich Miescher Institute Basel (Switzerland) Phone : +41 61 697 6492 Fax : +41 61 697 3976 Mail : michael.stadler at fmi.ch