This function is a wrapper around ggfastman::fast_manhattan which allows for the creation of a Manhattan plot from a dataframe containing GWAS summary statistics.
Usage
gg_manhattan_df(
sumstats_df,
annotation_df = NULL,
chr_col = chromosome,
pos_col = position,
pval_col = p_value,
pval_threshold = 0.001,
label_col = gene,
build = "hg19",
color1 = "#045ea7",
color2 = "#82afd3",
speed = "slow",
...
)Arguments
- sumstats_df
Dataframe containing GWAS summary statistics
- annotation_df
Optional dataframe containing chromosome, position, and annotation labels
- chr_col
Name of chromosome column
- pos_col
Name of position column
- pval_col
Name of p-value column
- pval_threshold
Threshold for plotting p-values (p-values greater than this value are excluded from the plot; default =
0.001)- label_col
Name of column in
annotation_dfcontaining annotations to include on the plot- build
(string) One of "hg18", "hg19", or "hg38" (passed to
ggfastman)- color1
(string) Color for odd-numbered chromosomes (passed to
ggfastman)- color2
(string) Color for even-numbered chromosomes (passed to
ggfastman)- speed
(string) One of "slow", "fast", or "ultrafast"; passed to
ggfastmanto control plotting speed- ...
Arguments passed to ggfastman::fast_manhattan
See also
Other plotting:
gg_qq_df()