View source: R/plot_regional.R
plot_regional | R Documentation |
A regional association plot is essentially a zoomed-in Manhattan plot, allowing the researcher to look at associations in a small, pre-defined area of the genome.
plot_regional(dataset, chr, start_pos, end_pos, plot_cutoff_p = 1, name_cutoff_p, data_name = NULL, save_name = "regional_association_plot", save_dir = getwd(), header_translations, main = "Regional association plot", ...)
dataset |
data frame containing the SNPs chromosome number,
position, p-value and (if a |
chr |
character or numeric value indicating the chromosome of interest. |
start_pos, end_pos |
Numeric; the position values of the beginning and end of the region of interest. |
plot_cutoff_p |
numeric - the threshold of p-values to be
shown in the QQ & Manhattan plots. Higher (less
significant) p-values are not included in the plot. Note
that, unlike in |
name_cutoff_p |
numeric; SNPs with p-values lower than or
equal to this value will have their names plotted in the
graph. If set to |
data_name |
character string; the subtitle for the plot. |
save_name |
character string; the filename, without extension, for the graph file. |
save_dir |
character string; the directory where the graph is saved. Note that R uses forward slash (/) where Windows uses backslash (\). |
header_translations |
translation table for column names.
See |
main, ... |
arguments passed to |
By default, plot_regional
expects dataset
to use the
standard column-names used by QC_GWAS
. A
translation table can be specified in header_translations
to allow non-standard names. See translate_header
for more information.
An invisible NULL
.
For creating a Manhattan plot: QC_plots
.
## Not run: data("gwa_sample") plot_regional(dataset = gwa_sample, chr = 2, start_pos = 55000000, end_pos = 75000000, data_name = "QC GWAS sample data", save_name = "sample_regional_association") ## End(Not run)
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