effect_plot: Create a plot comparing effects within two datasets

In wuxi-nextcode/topR: Create custom plots for viewing genetic association results using ggplot

Description

effect_plot()

Usage

effect_plot(
  dat,
  pheno_x = "x_pheno",
  pheno_y = "y_pheno",
  annotate_with = "Gene_Symbol",
  thresh = 1e-08,
  ci_thresh = 1,
  gene_label_thresh = 1e-08,
  color = get_topr_colors()[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	The name of the phenotype whose effect is plotted on the x axis
pheno_y	The name of the phenotype whose effect is plotted on the y axis
annotate_with	The name of the column that contains the label for the datapoints (default value is Gene_Symbol)
thresh	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	Show the confidence intervals if the P-value is below this threshold
gene_label_thresh	Label datapoints with P2 below this threshold
color	default value is the first of the topr colors

Examples

## Not run: 
effect_plot(dat)

## End(Not run)

wuxi-nextcode/topR documentation built on Dec. 23, 2021, 6:13 p.m.