regionplot() displays the association results for a smaller genetic regions within one chromosome.
Required parameter is at least one dataset (dataframe) containing the association data (with columns CHROM,POS,P in upper or lowercase) and either a variant ID, gene name or the genetic region represented as a chromosome together with start and stop positions (either as a single string or as three separate arguments).
All other input parameters are optional
Usage
regionplot(
df,
ntop = 10,
annotate = NULL,
xmin = 0,
size = 2,
shape = 19,
alpha = 1,
label_size = 4,
annotate_with = "ID",
color = get_topr_colors(),
axis_text_size = 11,
axis_title_size = 12,
title_text_size = 13,
show_genes = NULL,
show_overview = TRUE,
show_exons = NULL,
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 = 11,
nudge_x = 0.01,
nudge_y = 0.01,
rsids = NULL,
variant = NULL,
rsids_color = NULL,
legend_name = "",
legend_position = "right",
chr = NULL,
vline = NULL,
show_gene_names = NULL,
legend_labels = NULL,
gene = NULL,
title = NULL,
label_color = NULL,
locuszoomplot = FALSE,
region = NULL,
legend_nrow = NULL,
gene_label_size = NULL,
scale = 1,
show_legend = TRUE,
sign_thresh_linetype = "dashed",
sign_thresh_size = 0.5,
rsids_with_vline = NULL,
annotate_with_vline = NULL,
show_gene_legend = TRUE,
unit_main = 7,
unit_gene = 2,
unit_overview = 1.25,
verbose = NULL,
gene_color = NULL,
segment.size = 0.2,
segment.color = "black",
segment.linetype = "solid",
max.overlaps = 10,
unit_ratios = NULL,
extract_plots = FALSE,
label_fontface = "plain",
label_family = "",
gene_label_fontface = "plain",
gene_label_family = "",
build = 38,
label_alpha = 1,
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.- ntop
An integer, number of datasets (GWAS results) to show on the top plot
- annotate
A number (p-value). Display annotation for variants with p-values below this threshold
- 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.gvline=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
- locuszoomplot
A logical scalar set to FALSE. Only set to TRUE by calling the locuszoom function
- region
A string representing a genetic region, e.g. chr1:67038906-67359979
- legend_nrow
An integer, sets the number of rows allowed for the legend labels
- gene_label_size
A number setting the size of the gene labels shown at the bottom of the plot
- scale
A number, to change the size of the title and axes labels and ticks at the same time (default : 1)
- show_legend
A logical scalar, set to FALSE to hide the legend (default : TRUE)
- sign_thresh_linetype
A string, the line-type of the horizontal significance threshold (default : dashed)
- sign_thresh_size
A number, sets the size of the horizontal significance threshold line (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
- show_gene_legend
A logical scalar, set to FALSE to hide the gene legend (default value is TRUE)
- unit_main
the height unit of the main plot (default = 7)
- unit_gene
the height unit of the gene plot (default= 2 )
- unit_overview
the height unit of the overview plot (default = 1.25)
- verbose
Logical, set to FALSE to get suppress printed information
- 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)
- max.overlaps
Exclude text labels that overlap too many things. Defaults to 10 (ggrepel argument)
- unit_ratios
A string of three numbers separated by ":", for the overview, main and gene plots height ratios e.g 1.25:7:2
- 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).
- label_alpha
An number or vector of numbers to set the transparency of the plot labels (default:
label_alpha=1)- 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.