bacsnp.plot | R Documentation |
Function to draw a SNP frequency plot. Requires ggplot2.
bacsnp.plot(
x,
col = "SPEC",
genome.length = NULL,
mark.repeats = NULL,
mark.lowGQ = NULL,
mark.lowQUAL = NULL
)
x |
A VCF dataframe that contains the SNP data from a single isolate only. vcf_transformation. |
col |
Column of the dataframe which is used to colorize each SNP position. |
genome.length |
The length of the reference genome. If set to default the last SNP position is used. |
mark.repeats |
Dataframe that contains the repeat regions of the genome. |
mark.lowGQ |
Numeric value >= 0 |
mark.lowQUAL |
Numeric value >= 0 |
A list of two elements. First element is the input dataframe with SNP specificities added. The second element is a counting talbe with all SNP specificity combinations.
## Not run:
iso1 <- bac[bac$ISO == "iIsolate1",]
bacsnp.plot(iso1, col = "SPEC")
bacsnp.plot(iso1, col = "SPEC", genome.length = 125000)
## End(Not run)
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