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PheWAS plot

Source: R/fig_phewas.R
fig_phewas.Rd

fig_phewas creates a plot visualising results from phenome-wide association studies (PheWAS).

Usage

fig_phewas(
  data,
  groups = NULL,
  colours = NULL,
  interactive = FALSE,
  thresh = 1e-05,
  thresh_size = 0.5,
  trunc = 1e-30,
  point_size = 2,
  group_dist = 0.05,
  x_labels = TRUE,
  label_top = TRUE,
  label_thresh = 1e-05,
  label_n = NULL,
  label_size = 3,
  label_ymax = 1e-05,
  label_box = FALSE,
  label_nudge_x = 0,
  label_nudge_y = 0,
  title = NULL,
  title_size = NULL,
  title_center = FALSE,
  axis_text_size = NULL,
  axis_text_angle = -60,
  axis_title_size = NULL,
  legend = FALSE,
  legend_title = "Group",
  legend_text_size = NULL,
  legend_title_size = NULL,
  legend_point_size = NULL,
  legend_spacing_size = NULL,
  limit_padding = 20,
  plot_width = 9,
  plot_height = 6,
  girafe = TRUE
)

Arguments

data

a data.frame containing the association statistics for each phenotype with the following columns:

  • pvalue the association p-value for each phenotype

  • sign the direction of the association with the phenotype, where 0 = missing, 1 positive association, -1 negative association

  • group the phenotype group for each phenotype

  • label the optional point labelling variable (e.g. phenotype name), if label = "" for a point then no label is presented for that point

  • text the optional hover text variable for interactive plots to display further information, if text = "" for a point then no hover text is presented for that point

groups

a character vector of groups describing the grouping variable in data (default: NULL)

colours

a character vector of colours corresponding to defined groups (default: NULL)

interactive

a logical value indicating whether the plot should be interactive (default: FALSE)

thresh

a numeric value providing the p-value threshold to be plotted (default: NULL)

thresh_size

a numeric value indicating the width of the lines indicating the p-value thresholds (default: 0.5)

trunc

a numeric value representing the maximum p-value for which results are displayed (default: 1e-30)

point_size

a numeric value indicating the size of each point (default: 2)

group_dist

a numeric value indicating the gap between different groups (default: 0.05)

x_labels

a logical value whether the x-axis should be labelled (default: TRUE)

label_top

a logical value whether the top associated points should be labelled (default: TRUE)

label_thresh

a numeric value providing a p-value threshold for labelling points (default: 1e-5)

label_n

an integer value providing a limit on the number of top associations to label (default: NULL)

label_size

a numeric value indicating the size of each label (default: 3)

label_ymax

a numeric value indicating the p-value threshold for the maximum y-axis value at which labels can be displayed (default: 1e-5)

label_box

a logical value indicating whether labels should be surrounded by a box (default: FALSE)

label_nudge_x

a numeric value indicating the degree to which label placement on the x-axis should be adjusted (default: 0)

label_nudge_y

a numeric value indicating the degree to which label placement on the y-axis should be adjusted (default: 0)`

title

a character string providing a title for the plot (default: NULL)

title_size

a numeric value indicating the size of the title text for the plot (default: NULL)

title_center

a logical value indicating whether the plot title should be centered (default: FALSE)

axis_text_size

a numeric value indicating the size of the axis text for the plot (default: NULL)

axis_text_angle

a numeric value indicating the angle of the text on the x-axis of the plot (default: -60)`

axis_title_size

a numeric value indicating the size of the axis title text for the plot (default: NULL)

legend

a logical value indicating whether a legend corresponding to the displayed groups should be included (default: FALSE)

legend_title

a character string providing a title for the legend (default: "Group")

legend_text_size

a numeric value indicating the size of the legend text (default: NULL)

legend_title_size

a numeric value indicating the size of the legend title (default: NULL)

legend_point_size

a numeric value indicating the size of each point within the legend (default: NULL)

legend_spacing_size

a numeric value indicating spacing of points present in the legend (default: NULL)

limit_padding

a numeric value indicating the relative distance of plotted points from x-axis extremes (default: 20)

plot_width

a numeric value indicating the width of the PheWAS plot (default: 9)

plot_height

a numeric value indicating the height of the PheWAS plot (default: 6)

girafe

a logical value indicating whether an interactive plot should be turned into an interactive graphic using girafe() (default = TRUE)

Value

fig_phewas returns a PheWAS plot for phenome-wide association studies.

Details

This plotting function visualises results from phenome-wide association studies (PheWAS) in the form of a Manhattan style plot. Associations are grouped into phenotype categories. By default the results are truncated using a p-value cut-off of 1e-30.

Author

James Staley jrstaley95@gmail.com

Examples

fig_phewas(
  data = geni.plots::geni_test_phewas,
  axis_text_angle = -85,
  axis_text_size = 8
)