Package 'geni.plots' reference manual

Title:	GENI plots
Description:	GENI plots is designed to visualise results from genome-wide association studies.
Authors:	James Staley [aut, cre] , Wes Spiller [aut] , Tom Palmer [ctb]
Maintainer:	James Staley <[email protected]>
License:	GPL-3
Version:	0.1.1
Built:	2024-10-02 04:43:36 UTC
Source:	https://github.com/jrs95/geni.plots

Manhattan plot

Description

fig_manhattan creates a Manhattan plot for genomic markers from across the genome, e.g. results from genome-wide association studies.

Usage

fig_manhattan(
  data,
  colours = c("#7395D3", "#1D345D"),
  rank_pos = FALSE,
  thin_thresh = NULL,
  block_thresh = NULL,
  interactive = FALSE,
  interactive_n = NULL,
  thresh = c(1e-05, 5e-08),
  thresh_size = 0.5,
  thresh_colours = c("grey50", "red"),
  trunc = 1e-30,
  highlight_colours = NULL,
  point_size = 2,
  chr_dist = 1e+07,
  x_labels = TRUE,
  label_top = TRUE,
  label_thresh = 1e-05,
  label_size = 3,
  label_ylim = -log10(1e-05),
  label_nudge_y = 0,
  label_box = FALSE,
  title = NULL,
  title_size = NULL,
  title_center = FALSE,
  axis_text_size = NULL,
  axis_title_size = NULL,
  plot_width = 16,
  plot_height = 8,
  girafe = TRUE
)
fig_manhattan(
  data,
  colours = c("#7395D3", "#1D345D"),
  rank_pos = FALSE,
  thin_thresh = NULL,
  block_thresh = NULL,
  interactive = FALSE,
  interactive_n = NULL,
  thresh = c(1e-05, 5e-08),
  thresh_size = 0.5,
  thresh_colours = c("grey50", "red"),
  trunc = 1e-30,
  highlight_colours = NULL,
  point_size = 2,
  chr_dist = 1e+07,
  x_labels = TRUE,
  label_top = TRUE,
  label_thresh = 1e-05,
  label_size = 3,
  label_ylim = -log10(1e-05),
  label_nudge_y = 0,
  label_box = FALSE,
  title = NULL,
  title_size = NULL,
  title_center = FALSE,
  axis_text_size = NULL,
  axis_title_size = NULL,
  plot_width = 16,
  plot_height = 8,
  girafe = TRUE
)

Arguments

`data`	a `data.frame` containing the chromosome-position information and association statistics for each genomic marker (e.g., genetic variants) with the following columns: `chr` the chromosome for each genomic marker `pos` the genomic position for each genomic marker `pvalue` the association p-value for each genomic marker `highlight` the optional highlight points variable, where `0` = point not highlighted, `1` = first highlight colour, `2` = second highlight colour, etc. `highlight_shape` the optional highlight point shape variable, where `0` = standard circle, `1` = standard circle with border, `2` = standard rectangle, `3` = standard rectangle with border, `4` = standard diamond, `5` = standard diamond with border `label` the optional point labelling variable (e.g. gene 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
`colours`	a `vector` of colours used to differentiate chromosomes, these can either be a separate colour for each chromosome or a pair of colours (default: `c("#7395D3", "#1D345D")`)
`rank_pos`	a `logical` value whether genomic markers should be plotted by their rank position (default: `FALSE`)
`thin_thresh`	a `numeric` value representing the minimum p-value threshold for genomic markers to be displayed (default: `NULL`)
`block_thresh`	a `numeric` value for representing a p-value threshold, above which genomic markers are represented using blocks of colour (default: `NULL`)
`interactive`	a `logical` value indicating whether the plot should be interactive (default: `FALSE`)
`interactive_n`	a `numeric` value indicating the number of top associated points (max = 100,000) to present before using blocks of colour to minimise file size (default: `NULL`)
`thresh`	a `numeric` `vector` providing p-value thresholds to be plotted (default: `c(1e-5, 5e-8)`)
`thresh_size`	a `numeric` value indicating the width of the lines indicating the p-value thresholds (default: `0.5`)
`thresh_colours`	a `character` `vector` indicating the colours of the lines indicating the p-value thresholds (default: `c("grey50", "red")`)
`trunc`	a `numeric` value representing the maximum p-value for which results are displayed (default: `1e-30`)
`highlight_colours`	a `vector` indicating the colours for the highlighted genomic markers (default: `NULL`)
`point_size`	a `numeric` value indicating the size of each point (default: `2`)
`chr_dist`	a `numeric` value indicating the gap between different chromosomes (default: `10000000`)
`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_size`	a `numeric` value indicating the size of each label (default: `3`)
`label_ylim`	a `numeric` value indicating maximum y-axis value at which labels can be displayed (default: `-log10(1e-5)`)
`label_nudge_y`	a `numeric` value indicating the degree to which label placement on the y-axis should be adjusted (default: `0`)'
`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 `numeric` 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`)
`plot_width`	a `numeric` value indicating the width of the plot (default: `16`)
`plot_height`	a `numeric` value indicating the height of the plot (default: `8`)
`girafe`	a `logical` value indicating whether an interactive plot should be turned into an interactive graphic using girafe() (default = `TRUE`)

Details

This plotting function plots a Manhattan plot for genomic markers from across the genome. The default is to truncate these results to p-value cut-off of 1e-30.

Value

fig_manhattan returns a Manhattan plot for genomic markers from across the genome, e.g. results from genome-wide association studies.

Author(s)

James Staley [email protected]

Examples

fig_manhattan(
  data = geni.plots::geni_test_manhattan,
  block_thresh = 1e-4,
  label_box = TRUE
)

fig_manhattan(
  data = geni.plots::geni_test_manhattan,
  block_thresh = 1e-4,
  label_box = TRUE
)

PheWAS plot

Description

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
)
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`)

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.

Value

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

Author(s)

James Staley [email protected]

Examples

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

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

QQ plot

Description

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
)
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`)

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.

Value

fig_qq returns a quantile-quantile plot.

Author(s)

James Staley [email protected]

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
)

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
)

Regional plot

Description

fig_region creates a regional plot, i.e. a scatter graph of genomic markers associations (e.g. log10(p-values)) with a gene bar underneath.

Usage

fig_region(
  data,
  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 = NULL,
  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 = 9,
  plot_height = 7,
  girafe = TRUE
)
fig_region(
  data,
  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 = NULL,
  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 = 9,
  plot_height = 7,
  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` the association p-value for each genomic marker `z` the association z-statistic for each genomic marker `prob` the association probability for each genomic marker
`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`	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: `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: `12`)
`legend_title_size`	a `numeric` value indicating the size of the legend title (default: `12`)
`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: `9`)
`plot_height`	a `numeric` value indicating the height of the plot (default: `7`)
`girafe`	a `logical` value indicating whether an interactive plot should be turned into an interactive graphic using girafe() (default = `TRUE`)

Value

fig_region returns a regional plot visualising associations of markers within a genomic region.

Author(s)

James Staley [email protected]

Examples

fig_region(
  data = geni.plots::geni_test_region$assoc,
  corr = geni.plots::geni_test_region$corr,
  build = 37,
  axis_text_size = 11,
  axis_title_size = 12,
  genebar_label_size = 3.5,
  legend_text_size = 10,
  legend_title_size = 10
)

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

fig_region(
  data = geni.plots::geni_test_region$assoc,
  corr = geni.plots::geni_test_region$corr,
  build = 37,
  axis_text_size = 11,
  axis_title_size = 12,
  genebar_label_size = 3.5,
  legend_text_size = 10,
  legend_title_size = 10
)

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

Regional plot save

Description

fig_region_save saves the regional plots to file.

Usage

fig_region_save(
  fig,
  file,
  ntraits = 1,
  interactive = FALSE,
  width = NULL,
  height = NULL,
  dpi = 500
)
fig_region_save(
  fig,
  file,
  ntraits = 1,
  interactive = FALSE,
  width = NULL,
  height = NULL,
  dpi = 500
)

Arguments

`fig`	a regional plot object
`file`	a `character` string of the file path to save the plot
`ntraits`	an `integer` value of the number of traits plotted (default: `1`)
`interactive`	a `logical` value indicating whether the plot is interactive (default: `FALSE`)
`width`	a `numeric` value indicating the width of the plot in inches (default: `NULL`)
`height`	a `numeric` value indicating the height of the plot in inches (default: `NULL`)
`dpi`	the resolution of the plot (default: `500`)

Author(s)

James Staley [email protected]

Examples

## Not run: 
fig <- fig_region(
  data = geni.plots::geni_test_region$assoc,
  corr = geni.plots::geni_test_region$corr,
  build = 37
)
fig_region_save(fig, "test.png")

## End(Not run)
## Not run: 
fig <- fig_region(
  data = geni.plots::geni_test_region$assoc,
  corr = geni.plots::geni_test_region$corr,
  build = 37
)
fig_region_save(fig, "test.png")

## End(Not run)

Stacked regional plot

Description

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
)
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(s)

James Staley [email protected]

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

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

GENI plots test data for the Manhattan plot

Description

An R object containing formatted results from a genome-wide association study (GWAS) of interleukin-6 levels with p-values < 1e-3 (GCST90274815).

Usage

geni_test_manhattan
geni_test_manhattan

Format

A data.frame containing the variables necessary for constructing a static Manhattan plot. Specifically, this includes the following information:

chr the chromosome for each genomic marker
pos the genomic position (GRCh37) for each genomic marker
pvalue the association p-value for each genomic marker
highlight an indicator variable whether the genomic marker should be highlighted: 0 = point not highlighted, 1 = first highlight colour
highlight_shape an indicator variable of the illustrated shape for the genomic markers: 0 = standard circle, 5 = standard diamond with border
label the name of the nearest gene for each sentinel genome-wide associated genetic variant, the labels for non-sentinel genetic variants are omitted

Author(s)

James Staley [email protected]

Wes Spiller

Examples

head(geni_test_manhattan)

head(geni_test_manhattan)

GENI plots test data for the PheWAS plot

Description

An R object containing formatted data from a phenome-wide association study (PheWAS) of rs2228145 (1:154426970-A-C) from FinnGen r9.

Usage

geni_test_phewas
geni_test_phewas

Format

A data.frame containing the variables necessary for constructing an interactive PheWAS plot. Specifically, this includes the following information:

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 phenotype name
text the hover text containing further information on the association including: phenotype, phenotypic category, genetic variant ID, direction of association, association p-value, number of cases and number of controls

Author(s)

James Staley [email protected]

Wes Spiller

Examples

head(geni_test_phewas)

head(geni_test_phewas)

GENI plots test data for the regional plot

Description

An R object containing formatted results from a genome-wide association study (GWAS) of interleukin-6 levels (GCST90274815) and linkage disequilibrium statistics from 1000 Genomes Phase 3 for the region 1:154301970-154551970.

Usage

geni_test_region
geni_test_region

Format

A list containing 2 objects with the information necessary for constructing an interactive regional plot. Specifically, this includes the following information:

assoc a data.frame with genetic association results for interleukin-6 levels from GCST90274815 for the region 1:154301970-154551970
corr a matrix of Pearson correlation statistics (not squared) from the European samples of 1000 Genomes Phase 3 for the region 1:154301970-154551970, this matrix has the same markers in the same order as assoc

Details

assoc is a data.frame with the following columns:

marker the genomic marker identifier (i.e. rsID or chromosome-position)
chr the chromosome for each genomic marker
pos the genomic position (GRCh37) for each genomic marker
pvalue the association p-value for each genomic marker

Author(s)

James Staley [email protected]

Wes Spiller

Examples

head(geni_test_region$assoc)
head(geni_test_region$corr)

head(geni_test_region$assoc)
head(geni_test_region$corr)

GENI plots test data for the stacked regional plot

Description

An R object containing formatted results from genome-wide association studies (GWAS) of interleukin-6 levels (GCST90274815) and interleukin-6 receptor levels (GCST90088597) and linkage disequilibrium statistics from 1000 Genomes Phase 3 for the region 1:154301970-154551970.

Usage

geni_test_stack_region
geni_test_stack_region

Format

A list containing 2 objects with the information necessary for constructing an interactive stacked regional plot. Specifically, this includes the following information:

assoc a data.frame with genetic association results for interleukin-6 levels from GCST90274815 and for interleukin-6 receptor levels GCST90088597 for the region 1:154301970-154551970
corr a matrix of Pearson correlation statistics (not squared) from the European samples of 1000 Genomes Phase 3 for the region 1:154301970-154551970, this matrix has the same markers in the same order as assoc

Details

assoc is a data.frame with the following columns:

marker the genomic marker identifier (i.e. rsID or chromosome-position)
chr the chromosome for each genomic marker
pos the genomic position (GRCh37) for each genomic marker
pvalue_1 the association p-value for interleukin-6 levels for each genomic marker
pvalue_2 the association p-value for interleukin-6 receptor levels for each genomic marker

Author(s)

James Staley [email protected]

Wes Spiller

Examples

head(geni_test_stack_region$assoc)
head(geni_test_stack_region$corr)

head(geni_test_stack_region$assoc)
head(geni_test_stack_region$corr)

Package 'geni.plots'

Help Index

Manhattan plot

Description

Usage

Arguments

Details

Value

Author(s)

Examples

PheWAS plot

Description

Usage

Arguments

Details

Value

Author(s)

Examples

QQ plot

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Regional plot

Description

Usage

Arguments

Value

Author(s)

Examples

Regional plot save

Description

Usage

Arguments

Author(s)

Examples

Stacked regional plot

Description

Usage

Arguments

Value

Author(s)

Examples

GENI plots test data for the Manhattan plot

Description

Usage

Format

Author(s)

Examples

GENI plots test data for the PheWAS plot

Description

Usage

Format

Author(s)

Examples

GENI plots test data for the regional plot

Description

Usage

Format

Details

Author(s)

Examples

GENI plots test data for the stacked regional plot

Description

Usage

Format

Details

Author(s)

Examples