View source: R/gtable_associations.R
gtable_ld_associations | R Documentation |
Creates a gtable of a linkage disequilibrium, chromosomic positions, and association scores ggplots.
gtable_ld_associations(
df_assocs,
df_ld,
pvalue_colname = "pvalues",
labels_colname = "probe_id",
n_labels = 5,
diamonds = nrow(df_assocs) <= 40,
linked_area = diamonds,
point_size = 150/nrow(df_assocs),
colors = snp_position_colors(nrow(df_assocs)),
...
)
df_assocs |
SNP annotation data frame with columns chromosome, position, and as specified by parameters pvalue_colname and optionally labels_colname. |
df_ld |
Data frame with columns SNP_A, SNP_B, and R2, as returned by the snprelate_ld function. |
pvalue_colname |
Column name of df_snp with association values |
labels_colname |
Optional column name of df_snp with labels. Set NULL to remove labels. |
n_labels |
Number of labels of most associated SNPs to display. |
diamonds |
Should the values be displayed as diamonds or points ? Default is TRUE for up to 40 SNPs. |
linked_area |
Add a linked area to associations points. Default same as diamonds. |
point_size |
Point size for ggplot_ld, ignored if diamonds is TRUE. |
colors |
Colors of SNPs |
... |
Passed to ggplot_associations |
gtable
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