how i can make genetic marker frequency plot?
how I can create one plot using this data for more than one chromosome?
1. CHR Marker_ID A B FRECUENCY_A FRECUENCY_B
2. 1 0 120 163 0.424028269 0.575971731
3. 1 28511 138 179 0.43533123 0.56466877
4. 1 80849 132 184 0.417721519 0.582278481
5. 1 131493 134 188 0.416149068 0.583850932
6. 2 174364 134 167 0.445182724 0.554817276
7. 2 227341 140 174 0.445859873 0.554140127
8. 2 489290 125 154 0.448028674 0.551971326
9. 2 519811 141 166 0.459283388 0.540716612
10. 2 546093 141 169 0.45483871 0.54516129
11. 5 0 111 165 0.402173913 0.597826087
12. 5 10574371 128 186 0.407643312 0.592356688
13. 5 24590938 110 162 0.404411765 0.595588235
14. 5 25139346 117 169 0.409090909 0.590909091
15. 5 25453449 118 174 0.404109589 0.595890411
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danielmatsusaka •
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danielmatsusaka •
1 answer
Hi
If you are trying to plot the frequencies (FRECUENCY_A and FRECUENCY_B) along the genome, take a look at karyoploteR. With kpPoints you should be able to plot your frequencies and get something like this
It takes care of the multiple chromosomes and you can plot one on top of the other or all in a single line. In any case, if you'd like to plot them in a different way you can refer to the karyoploteR tutorial or just ask here :)
A couple of examples of other uses of kpPoints
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Can you please link us to an example of a 'genetic marker frequency plot' ?