effectplot {topr}

Create a plot comparing variant effects in two datasets

Description

effectplot()

Usage

effectplot(
  df,
  pheno_x = "x_pheno",
  pheno_y = "y_pheno",
  annotate_with = "Gene_Symbol",
  thresh = 5e-08,
  ci_thresh = 1,
  gene_label_thresh = 5e-08,
  color = get_topr_colors()[1],
  scale = 1,
  build = 38,
  label_fontface = "italic",
  label_family = "",
  nudge_y = 0.001,
  nudge_x = 0.001,
  size = 2,
  segment.size = 0.2,
  segment.linetype = "solid",
  segment.color = "transparent",
  angle = 0,
  title = NULL,
  axis_text_size = 10,
  axis_title_size = 12,
  title_text_size = 13,
  subtitle_text_size = 11,
  gene_label_size = 3.2,
  snpset_thresh = 5e-08,
  snpset_region_size = 1e+06,
  max.overlaps = 10,
  annotate = 0,
  label_color = NULL
)

Arguments

df

The input dataframe (snpset) containing one row per variant and P values (P1 and P2) and effects (E1 and E2) from two datasets/phenotypes OR a list containing two datasets.

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

Deprecated: A number, 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)

build

A number representing the genome build or a data frame. Set to 37 to change to build (GRCh37). The default is build 38 (GRCh38).

label_fontface

A string or a vector of strings. Label font “plain”, “bold”, “italic”, “bold.italic” (ggrepel argument)

label_family

A string or a vector of strings. Label font name (default ggrepel argument is "")

nudge_y

A number to horizontally adjust the starting position of each gene label (this is a ggrepel parameter)

nudge_x

A number to vertically adjust the starting position of each gene label (this is a ggrepel parameter)

size

A number or a vector of numbers, setting the size of the plot points (default: size=1.2)

segment.size

line segment color (ggrepel argument)

segment.linetype

line segment solid, dashed, etc.(ggrepel argument)

segment.color

line segment thickness (ggrepel argument)

angle

A number, the angle of the text label

title

A string to set the plot title

axis_text_size

A number, size of the x and y axes tick labels (default: 12)

axis_title_size

A number, size of the x and y title labels (default: 12)

title_text_size

A number, size of the plot title (default: 13)

subtitle_text_size

A number setting the text size of the subtitle (default: 11)

gene_label_size

A number setting the size of the gene labels shown at the bottom of the plot

snpset_thresh

A number representing the threshold used to create the snpset used for plotting (Only applicable if the input dataframe is a list containing two datasets)

snpset_region_size

A number representing the region size to use when creating the snpset used for plotting (Only applicable if the input dataframe is a list containing two datasets)

max.overlaps

Exclude text labels that overlap too many things. Defaults to 10 (ggrepel argument)

annotate

A number, label datapoints with p-value below below this number (in the second df) by their nearest gene

label_color

A string or a vector of strings. To change the color of the gene or variant labels

Value

ggplot object

Examples

## Not run: 
effectplot(list(CD_UKBB, CD_FINNGEN))

## End(Not run)