sqwwww
commented
10 months ago I was able to install the package/visualize the sample data correctly, however the dual synteny plotter is hitting an error with my custom data. I can visualize my ideogram file alone, which makes me thing the problem is the synteny data frame. I head that below and show the error.
`> head(xtrm.dual) Species_1 Start_1 End_1 Species_2 Start_2 End_2 fill 1 4 1217548 1218572 8078 25642678 25642943 ccccc 2 7 77444663 77457538 8134 58786633 58830026 ccccc 3 9 68868221 68871184 561 142495507 142515248 ccccc 4 3 136956088 136957125 7757 290722045 290804997 ccccc 5 3 70399900 70405443 4870 308049357 308056384 ccccc 6 10 50635257 50638250 8134 133443259 133454068 ccccc
ideogram(karyotype = xtrm.ideo, synteny = xtrm.dual) Error in if (synteny[i, 1] == "1") synteny[i, 8] <- 3.5 * 35.43307 + synteny[i, : missing value where TRUE/FALSE needed`
I am attaching the two data files used to generate the data. I will say using the read.table command provided was not sufficient for the above message, I tried to set the columns in my data to have the same class as the sample data, but that just changed from an undefined error to the current one.
just to remind people who have same problem, you can check your “synteny_dual_comparison”， probably some chromosomes are NA in this table.
I was able to install the package/visualize the sample data correctly, however the dual synteny plotter is hitting an error with my custom data. I can visualize my ideogram file alone, which makes me thing the problem is the synteny data frame. I head that below and show the error.
`> head(xtrm.dual) Species_1 Start_1 End_1 Species_2 Start_2 End_2 fill 1 4 1217548 1218572 8078 25642678 25642943 ccccc 2 7 77444663 77457538 8134 58786633 58830026 ccccc 3 9 68868221 68871184 561 142495507 142515248 ccccc 4 3 136956088 136957125 7757 290722045 290804997 ccccc 5 3 70399900 70405443 4870 308049357 308056384 ccccc 6 10 50635257 50638250 8134 133443259 133454068 ccccc
I am attaching the two data files used to generate the data. I will say using the read.table command provided was not sufficient for the above message, I tried to set the columns in my data to have the same class as the sample data, but that just changed from an undefined error to the current one.
xt.rm.dualcomp.txt trop.rana.4ideogram.txt