[genoPlotR-help] reading comparisons from blasts

[Lionel Guy]

Hi Peter,

On 11 May 2011, at 18:02 , Peter Neofotis wrote:

> I am stuck, though, on how to make the figure that you do in Example 4 of your vignette. I think my main confusion is that although you say you do the "comparison between four Bartonelle genomes using BLAST) it is not clear how this data is formatted when you load it for data(barto) - so I am confused when starting from scratch with my own data (from BLAST). 

You can find a complete description of the "barto" dataset by getting help on the barto object
> library(genoPlotR)
> ?barto

In short, it loads a barto object which is a list of 3, including 
- a list of 4 dna_seg object
- a list of 3 comparisons
- a further list of dna_segs that is not needed here

> Charophyte_Algae <- try(read_comparison_from_blast("/Users/pgn6/Desktop/R/CharaphyteAlgaeBlast.txt"))

You are loading only one file, whereas you should have one file per comparison (i.e Mesostigma_vs_Chlorokybus, Chlorokybus_vs_Chara, etc..)
> comp1 <- read_comparison_from_blast("Mesostigma_vs_Chlorokybus.blast")
> comp2 <- ...

> ## Plotting - this is the part that does not work. 
> plot_gene_map(dna_segs=list (Mesostigma, Chlorokybus, Chara, Chaetosphaeridium, Zygnema, Staurastrum), comparison = list(Charophyte_Algae), xlims=xlims, main = "Charaphyte Algae Internal Repeat", gene_type = "side_blocks", dna_seg_scale = TRUE, scale = FALSE)		

And here you need to have comparison=list(comp1, comp2, ...). 

In addition, looking at your files, it seems you are doing blastn, which is likely to yield very few results for organisms that are so far away. Try tblastx instead.

HTH,

Lionel