effect_plot()
This method is deprecated and will be removed in future versions. use effectplot instead.
Usage
effect_plot(
dat,
pheno_x = "pheno_x",
pheno_y = "pheno_",
annotate_with = "Gene_Symbol",
thresh = 1e-08,
ci_thresh = 1,
gene_label_thresh = 1e-08,
color = get_topr_colors()[1],
scale = 1
)Arguments
- dat
The input dataframe (snpset) containing one row per variant and P values (P1 and P2) and effects (E1 and E2) from two datasets/phenotypes
- pheno_x
A string representing the name of the phenotype whose effect is plotted on the x axis
- pheno_y
A string representing the name of the phenotype whose effect is plotted on the y axis
- annotate_with
A string, The name of the column that contains the label for the datapoints (default value is Gene_Symbol)
- thresh
A number. Threshold cutoff, datapoints with P2 below this threshold are shown as filled circles whereas datapoints with P2 above this threshold are shown as open circles
- ci_thresh
A number.Show the confidence intervals if the P-value is below this threshold
- gene_label_thresh
A string, label datapoints with P2 below this threshold
- color
A string, default value is the first of the topr colors
- scale
A number, to change the size of the title and axes labels and ticks at the same time (default = 1)