List of options
Compulsory flags:
One of snp, gene, or region must be specified to create the plot:
| Options |
Description |
Default value |
snp |
specify the SNP to be annotated (you must also include ignore.lead = TRUE if choosing this option) |
NA |
gene |
specify the Gene to make the plot around |
NA |
region |
specify the chromsome region you want to plot (must be specified as c(chr, start, end) |
NA |
data |
specify the data.frame (or a list of data.frames) to be used in the plot (requires the columns “CHR”, “BP”, “SNP”, and either “P” or “logBF”) |
NULL |
genes.data |
specify a data.frame with gene locations to plot beneath the graph (requires the columns “Gene”, “Chrom”, “Start”, and “End”) - the UCSC_GRCh37_Genes_UniqueList.txt in this repo can be used for this |
NA |
plot.title |
specify a title to go above your plot |
NA |
file.name |
specify a filename for your plot to be saved to |
NA |
Optional flags:
| Options |
Description |
Default value |
ld.file |
specify a data.frame with LD values relevant to the SNP specified by snp (requires the columns “SNP_B” and “R2”) |
NULL |
offset_bp |
specify how far either side of the snp, gene, or region you want the plot to extend |
200000 |
noncoding |
when using the UCSC gene list you can specify whether you want to plot the non-coding genes |
FALSE |
plot.type |
specify the file format of the plot (options are “jpg” or “svg”) |
“jpg” |
nominal |
specify the nominal significance level to draw on the plot (in -log10(P) |
|
significant |
specify the significance level to draw on the plot (in -log10(P) |
|
secondary.snp |
provide the list of secondary SNP IDs (must match IDs in results file) to be highlighted on the plot |
NA |
secondary.label |
specify whether to label the secondary SNPs on the plot |
FALSE |
genes.pvalue |
specify a data.frame of p-values (e.g. MAGMA results) associated with each gene (requires the columns “Gene” and “P”) |
NULL |
colour.genes |
specify whether to colour genes based on a p-value provided in gene.pvalue |
FALSE |
population |
specify the 1000 genomes population to use when calculating LD if ld.file = NULL (options are “AFR”, “AMR”, “EAS”, “EUR”, “SAS”, “TAMA”, and “ALL”) |
“EUR” |
sig.type |
specify whether the y-axis should be labelled as -log10(P) or log10(BF) (options are “P” or “BF”) |
“P” |
nplots |
specify whether multiple results plots will be saved into your jpeg file (e.g. plot two GWAS results one above another) |
FALSE |
ignore.lead |
specify whether to ignore the SNP with the smallest P and use the SNP specified by ‘snp’ to centre the plot |
FALSE |
rsid.check |
specify whether to check if the SNPs are labelled with rsIDs - should only matter if script is calculating LD for you |
TRUE |