How is the connection made between chromosomes in karyotype and synteny file?

[WimSpee]

Hi,

Thank you for the nice RIdeogram software. It is indeed difficult to find good and easy to use software for plotting synteny between 2 linear maps. This is what I hope that Rideogram can do.

I got the examples to work and also got some of my own data into a 2 way synteny plot.

I wonder how the connection is made between chromosomes in karyotype and synteny file?

In the the example code (also shown below) Roman numerals are used to identify the chromosomes in the karyotype file. In my own file I used chrX and lgX in this file. I am comparing a genetic and physical map.

In the synteny file normal (Arabic) numerals are used, and also required, otherwise the software runs into an error.

How does Rideogram know on which chromosome from the karytype file a line from the synteny file should be plotted? The chromosome names don't match up.

Is it also possible to manually line up the order of chromosomes between 2 maps? For example I know that chr1 corresponds to lg7 in my case, and the plot would be much nicer if chr1 and lg7 are direct below/above each other. Maybe even better with a straight instead of a curved line. Some chromosomes / linkage group maps could also be flipped, to get them in the same orientation (this is something that I also could do manually of course).

Thank you.

data(karyotype_dual_comparison, package="RIdeogram")
head(karyotype_dual_comparison)
#>   Chr Start      End   fill species size  color
#> 1  I      1 23037639 969696   Grape   12 252525
#> 2  II     1 18779884 969696   Grape   12 252525
#> 3 III     1 19341862 969696   Grape   12 252525
#> 4  IV     1 23867706 969696   Grape   12 252525
#> 5   V     1 25021643 969696   Grape   12 252525
#> 6  VI     1 21508407 0ab276   Grape   12 252525
table(karyotype_dual_comparison$species)
#> 
#>   Grape Populus 
#>      19      19

data(synteny_dual_comparison, package="RIdeogram")
head(synteny_dual_comparison)
#>   Species_1  Start_1    End_1 Species_2 Start_2   End_2   fill
#> 1         1 12226377 12267836         2 5900307 5827251 cccccc
#> 2        15  5635667  5667377        17 4459512 4393226 cccccc
#> 3         9  7916366  7945659         3 8618518 8486865 cccccc
#> 4         2  8214553  8242202        18 5964233 6027199 cccccc
#> 5        13  2330522  2356593        14 6224069 6138821 cccccc
#> 6        11 10861038 10886821        10 8099058 8011502 cccccc

[WimSpee]

If someone else runs into the same issue I found out how the connection is made. The numbers in the Species_1 and Species_2 columns of the synteny_dual_comparison files are just index numbers that point to the chromosomes defined for the 2 species defined in the karyotype_dual_comparison file.

To change the order of the chromosomes in the visualization, change the order of the chromosomes defined in the karyotype_dual_comparison file. And update the values in the Species_1 and Species_2 columns of the synteny_dual_comparison file accordingly.

@TickingClock1992 I think it would be more user friendly to connect to the chromosomes in the karyotype_dual_comparison by name instead of by index.

[TickingClock1992]

Thanks for suggestion. It is much easier to match these two files by index in the script. The 'Chr' column in karyotype file is just the name of corresponding chromosome while the row count corresponds to the chromosome number. And 'Species_1' and 'Species_2' columns in synteny file correspond to the chromosome numbers in their own species. In your case, you just need to put the lg7 in the first line of linkage group with 'Chr' being filled in 'lg7'. And in synteny file, using '1' in 'Species_1' to represent the 'chr1' and '1' in 'Species_2' to represent the 'lg7'. I think it will work in this way. And thanks for the suggestion again. I will try to make it more friendly for users in the next version.