The zoom.plot function creates a png file with a zoom in manhattan plot and LD plot.
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pvals |
a vector where each pval corresponds to a single SNP, ordered
by chromosome and position (same order as |
gene.id |
either a gene or phenotype name. If this matches a cis gene, that gene will be drawn in a different color. The name is also used for the plot title. |
all.snps |
a data.frame containing one row for each snp (same order as
pvals). The data.frame should have three named columns (in any order): id,
chrom, and position. The snp order should match |
snp.id |
The snp that the plot will center on. If not specified we find the most significant one |
genotypes |
a matrix of genotypes with 0/1/2 coding for all snps, with snps in columns |
window |
window size, in bp, of chromosomal region to show in zoom plot. If there are more than a few hundred SNPs it can be very slow to calculate LD. |
min.snps |
This argument is included for compatibility with previous versions but DOES NOT DO ANYTHING. |
color |
This can be |
ld.opts |
list of optional arguments for ld.matrix |
ld.colors |
color scale for LD plot (default white->red) |
img.height |
height of saved image |
img.width |
width of saved image |
img.prefix |
Any additional image prefix desired, in addition to the gene.id which is always included. |
save.image |
(default TRUE) set to false to plot with current device. Can be used to plot within R or to save with a different image format. This function was previously implemented in a standalone script
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