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QQ plot

Source: R/fig_qq.R
fig_qq.Rd

fig_qq creates a quantile-quantile (QQ) plot.

Usage

fig_qq(
  pvalues = NULL,
  group = NULL,
  data = NULL,
  groups = NULL,
  colours = NULL,
  interactive = FALSE,
  thresh = NULL,
  sample = FALSE,
  sample_thresh = 0.1,
  sample_prop = 0.1,
  ci = TRUE,
  ci_alpha = 0.05,
  ci_print = FALSE,
  inf_factor = FALSE,
  point_size = 3,
  label_top = FALSE,
  label_thresh = 1e-05,
  label_n = 10,
  label_size = 3.25,
  label_xlim = NULL,
  label_box = FALSE,
  title = NULL,
  title_size = NULL,
  title_center = FALSE,
  axis_text_size = NULL,
  axis_title_size = NULL,
  legend = TRUE,
  legend_title = "Group",
  legend_text_size = NULL,
  legend_title_size = NULL,
  legend_point_size = NULL,
  legend_spacing_size = NULL,
  ymax = NULL,
  plot_width = 6,
  plot_height = 6,
  girafe = TRUE
)

Arguments

pvalues

the association p-value for each marker (default: NULL)

group

a character vector determining the observation group for each marker (default: NULL)

data

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

  • pvalue the association p-value for each marker

  • group the optional grouping variable for each marker

  • label the optional point labelling variable (e.g. genomic marker), 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)

sample

a logical value indicating whether a random subset of p-values above the plotting threshold should be plotted, the number of which is controlled by sample_prop (default = FALSE)

sample_thresh

a numeric value indicating the p-value threshold defining the sample from which additional observations are selected (default: 0.1)

sample_prop

a numeric value indicating the proportion of sampled observations to be plotted (default: 0.1)

ci

a logical value indicating whether confidence intervals should be displayed (default: TRUE)

ci_alpha

a numeric value providing the threshold defining the plotted confidence interval (default: 0.05)

ci_print

a logical value indicating whether the proportion of points contained within the confidence interval band should be printed (default: FALSE)

inf_factor

a logical value indicating whether the inflation factor should be added to the plot (default: FALSE)

point_size

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

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_xlim

a numeric value indicating maximum x-axis value at which labels can be displayed (default: NULL)

label_box

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

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_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)

ymax

a numeric value defining the maximum value of the y-axis (default: NULL)

plot_width

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

plot_height

a numeric value indicating the height of the 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_qq returns a quantile-quantile plot.

Details

This plotting function plots a quantile-quantile plot of -log10(p-values). Observations can be divided into groups and can include corresponding confidence intervals. This plot is based on the QQ plot by Matthew Flickinger.

Author

James Staley jrstaley95@gmail.com

Examples

fig_qq(
  pvalues = geni.plots::geni_test_phewas$pvalue
)


fig_qq(
  data = geni.plots::geni_test_phewas[, c("pvalue", "group", "label", "text")],
  legend_title = "Category",
  legend_title_size = 10,
  legend_text_size = 8
)