User: Hu, Ying NIH/NCI [E]

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Posts by Hu, Ying NIH/NCI [E]

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Answer: A: How to represent a relationship between physical map and linkage map of a sequen
... ## please try the following codes library (OmicCircos) options (stringsAsFactors=FALSE) ; set.seed(1234) ; seg1   <- rep(paste0("Dr", 1:25), each=70); seg2   <- rep(paste0("LG", 1:25), each=70); segs   <- c(seg1, seg2); end    <- rep(1:70, 50); start  <- end - 1; seg.f <- data. ...
written 20 months ago by Hu, Ying NIH/NCI [E]50
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News: OmicCircos was updated
... Dear R/BioConductor Users, OmicCircos package was updated in the development version at http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html Thanks Ying yhu@mail.nih.gov ...
visualization news omiccircos written 2.8 years ago by Hu, Ying NIH/NCI [E]50
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Answer: A: RCircos 2D track plot for a small region of genome
... By the updated version, http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html, you can plot any genome regions by using the updated segAnglePo function. ...
written 2.8 years ago by Hu, Ying NIH/NCI [E]50
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Answer: A: OmicCircos mapping data file.
... OmicCircos was updated http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html Please let me know if you have any questions. Thanks Ying  yhu@mail.nih.gov ...
written 2.8 years ago by Hu, Ying NIH/NCI [E]50
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Answer: A: extdata missing for non-human OmicCircos plots?
... OmicCircos was updated http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html The output files are at https://www.dropbox.com/s/xgixwithokmedbq/BioC_ext.pdf?dl=0 and https://www.dropbox.com/s/inyrt19qvphjg2e/BioC_ext2.pdf?dl=0 by the following codes Thanks rm(list=ls()); library(" ...
written 2.8 years ago by Hu, Ying NIH/NCI [E]50
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Answer: A: Making a circos plot to show expression for a gene set rather than whole genome
... You maybe wanted one gene on one segment. Please try the code as the following.  The output file is at https://www.dropbox.com/s/pvudjol3s0wkde1/BioC_support01.pdf?dl=0 NOTE: Please use the updated version http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html rm(list=ls()); librar ...
written 2.8 years ago by Hu, Ying NIH/NCI [E]50
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Answer: A: How to specifiy colors for polygon links when using circos function of OmicCirco
... The issue is fixed in the updated package.  rm(list=ls()); library(OmicCircos); options(stringsAsFactors = FALSE); set.seed(1234); ## get chromosome information data("UCSC.hg19.chr", package="OmicCircos"); ref     <- UCSC.hg19.chr; ref[,1] <- gsub("chr", "", ref[,1]); ## initial values col ...
written 2.8 years ago by Hu, Ying NIH/NCI [E]50
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Answer: A: plotting both
... please try: zoom <- c(1, 1, start, end, 180, 358); "start" and "end" are the positions in which you wanted to zoom. Ying ________________________________________ From: Mark Carty [guest] [guest@bioconductor.org] Sent: Monday, February 03, 2014 10:47 AM To: bioconductor at r-project.org; mac449 ...
written 3.9 years ago by Hu, Ying NIH/NCI [E]50

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Scholar 20 months ago, created an answer that has been accepted. For A: How to represent a relationship between physical map and linkage map of a sequen

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