[genoPlotR-help] genoPlotR help

[Lionel Guy]

Dear Khalid,

Thanks for your interest in genoPlotR.
 From the top of my head, there are two ways of doing what you want to 
do. You can either use the argument dna_seg_labels in plot_gene_map:

plot_gene_map(dna_segs=list(pRra1, pRma, pRma1),
	      comparisons=list(pRra1_vs_pRma,pRra1_vs_pRma1),
  	      annotations=list(annots1,annots2,annots3),
               [...]
	      dna_seg_line=TRUE,
               dna_seg_labels=names)

or name the list of dna_segs prior to passing it to plot_gene_map:

dna_seg_list <- list(pRra1, pRma, pRma1)
names(dna_seg_list) <- names
plot_gene_map(dna_segs=dna_seg_list,
	      comparisons=list(pRra1_vs_pRma,pRra1_vs_pRma1),
  	      annotations=list(annots1,annots2,annots3),
               [...]
               )

Hope it helps. Let me know if it doesn't ;)

Cheers,

Lionel


On 08/05/2014 12:07 PM, Khalid EL KARKOURI wrote:
> Hi Dr. Guy,
>
> I am using genoPlotR that is the best software compared to all others tools published uptoday for the same purpuse.
>
> I have one difficulty which is to place the name of the chromosome near each chromosome in the figure (like species of B. baciliformis figure you did)
>
> Below my script; I have three genebank file and two comparison blast files. I used the script names <- c(species1, species2, species3) but it does not work.
>
> Could you please help me to resolve that ?
>
> Thank you very much for your help.
>
> Khalid
>
>
> ***********************************************************************
>
> ## Load library & data
>
> library(genoPlotR)
>
> ## Loding data
> pRra1 <- try (read_dna_seg_from_file("pRra1_reordoner_rev_complet.gbk"))
> pRma <- try (read_dna_seg_from_file("pRma.gbk"))
> pRma1 <- try (read_dna_seg_from_file("pRma.gbk"))
>
>
>
> ## Saving data
> imgPath <- "~/Documents/R/"
> pdfPath <- "~/Documents/R/"
>
> ## Comparison
>
> pRra1_vs_pRma <- try (read_comparison_from_blast("pRra1_vs_pRma.csv"))
> pRra1_vs_pRma1 <- try (read_comparison_from_blast("pRra1_vs_pRma.csv"))
>
> xlims <- list (c(1,21000), c(1,15000),c(1,15000))
>
> names <- c ("species1", "species2", "species3")
>
>
>
> ## Annotations on all the segments
> annots1 <- auto_annotate(pRra1, locus_tag_pattern=, names=pRra1$gene, keep_genes_only=FALSE, rot=40, col="blue")
> annots2 <- auto_annotate(pRma, locus_tag_pattern=, names=pRma$gene, keep_genes_only=FALSE, rot=40, col="blue")
> annots3 <- auto_annotate(pRma1, locus_tag_pattern=, names=pRma1$gene, keep_genes_only=FALSE, rot=40, col="blue")
>
>
>
> ## Plots
> plot_gene_map(dna_segs=list(pRra1, pRma, pRma1),
> 	      comparisons=list(pRra1_vs_pRma,pRra1_vs_pRma1),
>   	      annotations=list(annots1,annots2,annots3),
> 	      legend=,
> 	      annotation_height=2,
> 	      annotation_cex=0.8,
> 	      arrow_head_leng=,
> 	      xlims= xlims,
> 	      main ="",
> 	      gene_type ="arrows",
> 	      dna_seg_scale=TRUE,
> #	      global_color_scheme
> 	      scale=TRUE,
> 	      n_scale_ticks=7,
> 	      dna_seg_line=TRUE)
>
>
> ******************************************************
> Dr. Khalid El Karkouri, IGR
> Bioinformatics and Genomics of micro-organisms
> Faculté de médecine, La Timone, Marseille
> UMR URMITE UM63, CNRS7278, IRD 198 INSERM1095
> Mail: khalid.ELKARKOURI at univ-amu.fr
> ******************************************************
>