From guy.lionel at gmail.com Thu Oct 17 10:34:57 2013 From: guy.lionel at gmail.com (Lionel Guy) Date: Thu, 17 Oct 2013 10:34:57 +0200 Subject: [genoPlotR-help] genoplot In-Reply-To: <1381942979.194901152@f229.i.mail.ru> References: <1381942979.194901152@f229.i.mail.ru> Message-ID: Hi Denis, Thanks for your interest in genoPlotR. See my comments inline. On 16 Oct 2013, at 19:02 , denis goryunov wrote: > 1. > For example, We have 4 contigs (A,B,C,D) in 4 different genbank format files(A.gbk,B.gbk,C.gbk,D.gbk) and We desire to compare the contig A with each other contigs. > We can perform BLAST and get 3 files: > A_vs_B.blastout > A_vs_C.blastout > A_vs_D.blastout > Can We use the genoplot software to visualize this comparison? Yes, but you'd have to cheat a bit. One solution is to make a plot with the A segment in two different rows, like this: B A C A D Thus you get all comparisons to A. Easy, but you'd have to run some more blasts (B to A, C to A). And a bit cumbersome. The other possibility that I see would be to have for example C and D on the same line, like this: B A C // D but requires some more tinkering: - concatenating contigs C and D, recording the position of each start/end of contig (e.g. if contig C is 25 kb and contig D is 30, the start/end positions are now 1-25000 for C and 25001-30000 for D) - running a blast A to CD - running plot_gene_map with dna_segs=list(B, A, CD) and xlims=list(c(1,Inf), c(1,Inf), c(1, 25000, 25001, 30000)) Something along those lines... > 2. > Other example. > We also have 4 contigs (A,B,C & D) in 4 different genbank format files(A.gbk,B.gbk,C.gbk,D.gbk) . > We performed BLAST and got 3 files: > A_vs_B.blastout > B_vs_C.blastout > C_vs_D.blastout > How We should specify for the plot_gene_map function, that: > > pair of A.gbk & B.gbk files corresponds to A_vs_B.blastout file > > pair of B.gbk & C.gbk files corresponds to B_vs_C.blastout file > > pair of C.gbk & D.gbk files corresponds to C_vs_D.blastout file ? Hmm... not sure I'm following you. There is no hard link between dna_segs and comparisons, just the order in which they are entered. Thus, if you have obtained your dna_seg objects A to D using A <- read_dna_seg_from_file(file="A.gbk, etc...) and comparisons using A_vs_B <- read_comparisons_from_blast(file="A_vs_B.blastout", ...) Then using plot_gene_map(dna_segs=list(A, B, C, D), comparisons=list(A_vs_B, B_vs_C, C_vs_D) should just work. Is that what you were asking? > How We should specify for the plot_gene_map function which of genbank format files correspond to the annotation object (if I'll use it)? Again, this is input order-dependent: simply use plot_gene_map(dna_segs=list(A, B, C, D), comparisons=list(A_vs_B, B_vs_C, C_vs_D), annotations=list(A_annotation, B_annotation,...) > 3. > > Finally, I have some plot after execution the plot_gene_map function (see attachment). How I should determine where are contigs A, B, C and D, if dna_segs=list(A,B,C,D) ? Hmm... are you sure you input 4 dna_segs? On the plot I see just three. So if you used dna_segs=list(A, B, C), then A is on top and C at the bottom. > Can I little bit adjust my picture, so that the annotation labels don't overlap each other and don't walk out beyond of paper? Yes. Either - use a larger device size: pdf(file=file.pdf, w=8, h=11), - increase the space for annotations: plot_gene_map(annotation_height = 2, ...) - reduce font size: plot_gene_map(annotation_cex = 0.5) or any combination thereof. You can also play with the "rot" argument/attribute of the annotation. See ?annotation and ?auto_annotate. HTH, Lionel > Thank You in advance, > Dr. Denis Goryunov, > Institute of Physico-chemical biology, > Department of Evolutionary Biochemistry, > MSU > > > > -- Lionel Guy F?lhagsleden 13, SE-75324 Uppsala | email: guy.lionel at gmail.com | mobile: +46 (0)73 9760618 | phone: +46 (0)18 410 7398