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Stacked regional plot

Source: R/fig_region.R
fig_region_stack.Rd

fig_region_stack creates a stacked regional association plot.

Usage

fig_region_stack(
  data,
  traits,
  corr = NULL,
  corr_top = NULL,
  top_marker = NULL,
  r2 = FALSE,
  build = 38,
  prob = FALSE,
  interactive = FALSE,
  thresh = NULL,
  thresh_colour = "grey50",
  x_min = NULL,
  x_max = NULL,
  y_title = NULL,
  point_size = 3,
  alpha = 1,
  genebar = TRUE,
  genebar_ntracks = NULL,
  genebar_label_pos = 3.6,
  genebar_label_size = 4,
  genebar_line_size = 0.8,
  label_size = 3.5,
  highlights = NULL,
  highlights_cat = NULL,
  highlights_label = TRUE,
  highlights_shape = 22,
  highlights_nolabel_shape = 21,
  highlights_sort = TRUE,
  highlights_colours = NULL,
  highlights_title = "Group",
  title_size = 16,
  title_center = FALSE,
  axis_text_size = 14,
  axis_title_size = 16,
  legend = TRUE,
  legend_text_size = 12,
  legend_title_size = 12,
  point_padding = 0,
  nudge_x = 0,
  nudge_y = 0,
  nudge_y_top = 0.06,
  ylim_prob = 1,
  assoc_plot_size = NULL,
  genebar_plot_size = NULL,
  legend_plot_dist = NULL,
  plot_width = NULL,
  plot_height = NULL,
  girafe = TRUE
)

Arguments

data

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

  • marker the genomic marker identifier (e.g. rsID)

  • chr the chromosome for each genomic marker

  • pos the genomic position for each genomic marker and one of the following:

  • pvalue_1, pvalue_2, pvalue_3, etc. the association p-values for each genomic marker and trait

  • z_1, z_2, z_3, etc. the association z-statistics for each genomic marker and trait

  • prob_1, prob_2, prob_3, etc. the association probabilities for each genomic marker and trait

traits

a character vector of trait names

corr

a numeric matrix of correlation statistics between the markers (default: NULL)

corr_top

a numeric vector of correlation statistics between the top marker and the rest of the markers (default: NULL)

top_marker

a character value depicting the marker to plot the correlation statistics of the rest of the markers against (default: NULL)

r2

a logical value indicating whether the set of correlation statistics entered in corr or corr_top are squared (default: FALSE)

build

a numeric value indicating the genome build used to determine genomic position (default: 38 representing human assembly GRCh38)

prob

a logical value indicating whether probability statistics should be plotted instead of -log10(p-values) (default: FALSE)

interactive

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

thresh

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

thresh_colour

a character vector indicating the colours of the lines indicating the p-value thresholds (default: "grey50")

x_min

a numeric value depicting the minimum plotted x-axis value representing the start of the genomic region (default: NULL)

x_max

a numeric value depicting the maximum plotted x-axis value representing the end of the genomic region (default: NULL)

y_title

a character string defining the title of the y-axis (default: NULL)

point_size

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

alpha

a numeric value adjusting the opacity of colours representing the correlation statistics (default: 1)

genebar

a logical value indicating whether bars representing the genes should be included in the plot (default: TRUE)

genebar_ntracks

an integer value indicating the number of tracks to be included in the gene bar (default: NULL)

genebar_label_pos

a numeric value indicating the relative position of gene labels with respect to each gene bar (default: 3.6)

genebar_label_size

a numeric value defining the size of each gene label (default: 4.25)

genebar_line_size

a numeric value defining the line size of each gene bar (default: 0.8)

label_size

a numeric value indicating the size of each label (default: 3.5)

highlights

a character vector defining a set of markers to highlight in the plot (default: NULL)

highlights_cat

a character vector defining the category for each highlighted marker (default: NULL)

highlights_label

a logical value indicating whether highlighted points should be labelled (default: TRUE)

highlights_shape

a value defining the shape for highlighted points (default: 22)

highlights_nolabel_shape

a value defining the shape for points which are not highlighted (default: 21)

highlights_sort

a logical value indicating whether to sort highlight group label levels (default: TRUE)

highlights_colours

a character vector specifying colours for highlighted points (default: NULL)

highlights_title

a character string providing a title for the legend corresponding to the highlighted points (default: "Group")

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: 14)

axis_title_size

a numeric value indicating the size of the axis title text for the plot (default: 16)

legend

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

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)

point_padding

a numeric value indicating the relative distance of labels from plotted points (default: 0

nudge_x

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

nudge_y

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

nudge_y_top

a numeric value indicating the degree to which the top marker should be adjusted on the y-axis by a proportion of the y-axis limit (default: 0.06)

ylim_prob

a numeric value defining the upper y-axis limit for probability plots (default: 1)

assoc_plot_size

a numeric value determining the size of the association plot (default: NULL)

genebar_plot_size

a numeric value determining the size of the gene bar plot (default: NULL)

legend_plot_dist

a numeric value defining the distance and size of the legend from the bottom of the regional plot (default = NULL)

plot_width

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

plot_height

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

girafe

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

Value

fig_region_stack returns a stacked regional plot.

Author

James Staley jrstaley95@gmail.com

Examples

fig <- fig_region_stack(
  data = geni.plots::geni_test_stack_region$assoc,
  traits = c("Interleukin-6 levels", "Interleukin-6 receptor levels"),
  corr = geni.plots::geni_test_stack_region$corr,
  build = 37,
  highlights = "rs11265611",
  title_center = TRUE
)

# Notes:
#   (i) corr has to have the same markers as assoc in the same order
#   (ii) by default fig_region_stack assumes corr contains correlation
#        statistics that have not been squared