View source: R/genome_plotter.R
single.chr.plotter.w.ci | R Documentation |
This function takes the genome scan output from scan.h2lmm() and plots the whole genome and single chromosome zoom-ins for all the specified chromosomes. When multiple imputations are used, includes the 95% confidence band on the median in the zoomed-in plots.
single.chr.plotter.w.ci( scan.object, qtl.ci.object, ci.type, scan.type, these.col = c("#7BAFD4", "red"), scale = "Mb", alpha = 0.05 )
scan.object |
A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted. Expected to the scan of the actual data. |
qtl.ci.object |
A run.positional.scans() object. Should contain single chromosome scans from some form of sampling process, such as a parametric bootstrap. |
ci.type |
Positional confidence interval to be included in the title. Example: "Parametric Bootstrap". |
scan.type |
Scan type to be included in the title. Example: "ROP". |
these.col |
Colors to be used for individual artificial scans. |
scale |
DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either "Mb" or "cM" is expected. |
alpha |
DEFAULT: 0.05. The specified alpha level of the positional confidence interval. |
single.chr.plotter.w.ci()
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