locuszoom {topr}

Create a locuszoom-like plot

Description

locuszoom() displays the association results for a smaller region within one chromosome. Required parameter is at least one dataset (dataframe) containing the association data (with columns CHROM,POS,P in upper or lowercase)

Usage

locuszoom(
  df,
  annotate = NULL,
  ntop = 3,
  xmin = 0,
  size = 2,
  shape = 19,
  alpha = 1,
  label_size = 4,
  annotate_with = "ID",
  color = NULL,
  axis_text_size = 11,
  axis_title_size = 12,
  title_text_size = 13,
  show_genes = NULL,
  show_overview = FALSE,
  show_exons = FALSE,
  max_genes = 200,
  sign_thresh = 5e-08,
  sign_thresh_color = "red",
  sign_thresh_label_size = 3.5,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  protein_coding_only = FALSE,
  region_size = 1e+06,
  gene_padding = 1e+05,
  angle = 0,
  legend_title_size = 12,
  legend_text_size = 12,
  nudge_x = 0.01,
  nudge_y = 0.01,
  rsids = NULL,
  variant = NULL,
  rsids_color = "gray40",
  legend_name = "Data:",
  legend_position = "right",
  chr = NULL,
  vline = NULL,
  show_gene_names = NULL,
  legend_labels = NULL,
  gene = NULL,
  title = NULL,
  label_color = "gray40",
  region = NULL,
  scale = 1,
  rsids_with_vline = NULL,
  annotate_with_vline = NULL,
  sign_thresh_size = 0.5,
  unit_main = 7,
  unit_gene = 2,
  gene_color = NULL,
  segment.size = 0.2,
  segment.color = "black",
  segment.linetype = "solid",
  show_gene_legend = TRUE,
  max.overlaps = 10,
  extract_plots = FALSE,
  label_fontface = "plain",
  label_family = "",
  gene_label_fontface = "plain",
  gene_label_family = "",
  build = 38,
  verbose = NULL,
  show_legend = TRUE,
  label_alpha = 1,
  gene_label_size = NULL,
  vline_color = "grey",
  vline_linetype = "dashed",
  vline_alpha = 1,
  vline_size = 0.5,
  log_trans_p = TRUE
)

Arguments

df

Dataframe or a list of dataframes (required columns are CHROM,POS,P), in upper- or lowercase) of association results.

annotate

A number (p-value). Display annotation for variants with p-values below this threshold

ntop

An integer, number of datasets (GWAS results) to show on the top plot

xmin, xmax

Integer, setting the chromosomal range to display on the x-axis

size

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

shape

A number of a vector of numbers setting the shape of the plotted points

alpha

A number or a vector of numbers setting the transparency of the plotted points

label_size

An number to set the size of the plot labels (default: label_size=3)

annotate_with

A string. Annotate the variants with either Gene_Symbol or ID (default: "Gene_Symbol")

color

A string or a vector of strings, for setting the color of the datapoints on the plot

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)

show_genes

A logical scalar, show genes instead of exons (default show_genes=FALSE)

show_overview

A logical scalar, shows/hides the overview plot (default= TRUE)

show_exons

Deprecated : A logical scalar, show exons instead of genes (default show_exons=FALSE)

max_genes

An integer, only label the genes if they are fewer than max_genes (default values is 200).

sign_thresh

A number or vector of numbers, setting the horizontal significance threshold (default: sign_thresh=5e-8). Set to NULL to hide the significance threshold.

sign_thresh_color

A string or vector of strings to set the color/s of the significance threshold/s

sign_thresh_label_size

A number setting the text size of the label for the significance thresholds (default text size is 3.5)

ymin, ymax

Integer, min and max of the y-axis, (default values: ymin=0, ymax=max(-log10(df$P)))

protein_coding_only

A logical scalar, if TRUE, only protein coding genes are used for annotation

region_size

An integer (default = 20000000) (or a string represented as 200kb or 2MB) indicating the window size for variant labeling. Increase this number for sparser annotation and decrease for denser annotation.

gene_padding

An integer representing size of the region around the gene, if the gene argument was used (default = 100000)

angle

A number, the angle of the text label

legend_title_size

A number, size of the legend title

legend_text_size

A number, size of the legend text

nudge_x

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

nudge_y

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

rsids

A string (rsid) or vector of strings to highlight on the plot, e.g. rsids=c("rs1234, rs45898")

variant

A string representing the variant to zoom in on. Can be either an rsid, or a dataframe (with the columns CHROM,POS,P)

rsids_color

A string, the color of the variants in variants_id (default color is red)

legend_name

A string, use to change the name of the legend (default: None)

legend_position

A string, top,bottom,left or right

chr

A string or integer, the chromosome to plot (i.e. chr15), only required if the input dataframe contains results from more than one chromosome

vline

A number or vector of numbers to add a vertical line to the plot at a specific chromosomal position, e.g vline=204000066. Multiple values can be provided in a vector, e.g vline=c(204000066,100500188)

show_gene_names

A logical scalar, if set to TRUE, gene names are shown even though they exceed the max_genes count

legend_labels

A string or vector of strings representing legend labels for the input datasets

gene

A string representing the gene to zoom in on (e.g. gene=FTO)

title

A string to set the plot title

label_color

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

region

A string representing a genetic region, e.g. chr1:67038906-67359979

scale

A number, to change the size of the title and axes labels and ticks at the same time (default : 1)

rsids_with_vline

A string (rsid) or vector of strings to highlight on the plot with their rsids and vertical lines further highlighting their positions

annotate_with_vline

A number (p-value). Display annotation and vertical lines for variants with p-values below this threshold

sign_thresh_size

A number, sets the size of the horizontal significance threshold line (default : 1)

unit_main

the height unit of the main plot (default = 7)

unit_gene

the height unit of the gene plot (default= 2 )

gene_color

A string representing a color, can be used to change the color of the genes/exons on the geneplot

segment.size

line segment color (ggrepel argument)

segment.color

line segment thickness (ggrepel argument)

segment.linetype

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

show_gene_legend

A logical scalar, set to FALSE to hide the gene legend (default value is TRUE)

max.overlaps

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

extract_plots

Logical, FALSE by default. Set to TRUE to extract the three plots separately in a list

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 "")

gene_label_fontface

Gene label font “plain”, “bold”, “italic”, “bold.italic” (ggrepel argument)

gene_label_family

Gene label font name (default ggrepel argument is "")

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).

verbose

Logical, set to FALSE to get suppress printed information

show_legend

A logical scalar, set to FALSE to hide the legend (default : TRUE)

label_alpha

An number or vector of numbers to set the transparency of the plot labels (default: label_alpha=1)

gene_label_size

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

vline_color

A string. The color of added vertical line/s (default: grey)

vline_linetype

A string. The linetype of added vertical line/s (default : dashed)

vline_alpha

A number. The alpha of added vertical line/s (default : 1)

vline_size

A number.The size of added vertical line/s (default : 0.5)

log_trans_p

A logical scalar (default: TRUE). By default the p-values in the input datasets are log transformed using -log10. Set this argument to FALSE if the p-values in the datasets have already been log transformed.

Value

plots using egg (https://cran.r-project.org/web/packages/egg/vignettes/Ecosystem.html)

Examples

## Not run: 
locuszoom(R2_CD_UKBB)

## End(Not run)