colocboost (version 1.0.7)

colocboost_plot: Plot visualization plot from a ColocBoost output.

Description

colocboost_plot generates visualization plots for colocalization events from a ColocBoost analysis.

Usage

colocboost_plot(
  cb_output,
  y = "log10p",
  grange = NULL,
  plot_cos_idx = NULL,
  outcome_idx = NULL,
  plot_all_outcome = FALSE,
  plot_focal_only = FALSE,
  plot_focal_cos_outcome_only = FALSE,
  points_color = "grey80",
  cos_color = NULL,
  add_highlight = FALSE,
  add_highlight_idx = NULL,
  add_highlight_style = "vertical_lines",
  outcome_names = NULL,
  plot_cols = 2,
  variant_coord = FALSE,
  show_top_variables = FALSE,
  show_cos_to_uncoloc = FALSE,
  show_cos_to_uncoloc_idx = NULL,
  show_cos_to_uncoloc_outcome = NULL,
  plot_ucos = FALSE,
  plot_ucos_idx = NULL,
  title_specific = NULL,
  ylim_each = TRUE,
  outcome_legend_pos = "top",
  outcome_legend_size = 1.8,
  cos_legend_pos = c(0.05, 0.4, 0.1, 0.5),
  show_variable = FALSE,
  lab_style = c(2, 1),
  axis_style = c(2, 1),
  title_style = c(2.5, 2),
  ...
)

Value

Visualization plot for each colocalization event.

Arguments

cb_output

Output object from colocboost analysis

y

Specifies the y-axis values, default is "log10p" for -log10 transformed marginal association p-values.

grange

Optional plotting range of x-axis to zoom in to a specific region.

plot_cos_idx

Optional indices of CoS to plot

outcome_idx

Optional indices of outcomes to include in the plot. outcome_idx=NULL to plot only the outcomes having colocalization.

plot_all_outcome

Optional to plot all outcome in the same figure.

plot_focal_only

Logical, if TRUE only plots colocalization with focal outcome, default is FALSE.

plot_focal_cos_outcome_only

Logical, if TRUE only plots colocalization including at least on colocalized outcome with focal outcome, default is FALSE.

points_color

Background color for non-colocalized variables, default is "grey80".

cos_color

Optional custom colors for CoS.

add_highlight

Logical, if TRUE adds vertical lines at specified positions, default is FALSE

add_highlight_idx

Optional indices for add_highlight variables.

add_highlight_style

Optional style of add_highlight variables, default is "vertical_lines", other choice is "star" - red star.

outcome_names

Optional vector of outcomes names for the subtitle of each figure. outcome_names=NULL for the outcome name shown in data_info.

plot_cols

Number of columns in the plot grid, default is 2. If you have many colocalization. please consider increasing this.

variant_coord

Logical, if TRUE uses variant coordinates on x-axis, default is FALSE. This is required the variable names including position information.

show_top_variables

Logical, if TRUE shows top variables for each CoS, default is FALSE

show_cos_to_uncoloc

Logical, if TRUE shows colocalization to uncolocalized outcomes to diagnose, default is FALSE

show_cos_to_uncoloc_idx

Optional indices for showing CoS to all uncolocalized outcomes

show_cos_to_uncoloc_outcome

Optional outcomes for showing CoS to uncolocalized outcomes

plot_ucos

Logical, if TRUE plots also trait-specific (uncolocalized) sets , default is FALSE

plot_ucos_idx

Optional indices of trait-specific (uncolocalized) sets to plot when included

title_specific

Optional specific title to display in plot title

ylim_each

Logical, if TRUE uses separate y-axis limits for each plot, default is TRUE

outcome_legend_pos

Position for outcome legend, default is "top"

outcome_legend_size

Size for outcome legend text, default is 1.2

cos_legend_pos

Proportion of the legend from (left edge, bottom edge) following by the distance for multiple labels (horizontal-x space, vertical-y space), default as (0.05, 0.4, 0.1, 0.5) at the left - median position

show_variable

Logical, if TRUE displays variant IDs, default is FALSE

lab_style

Vector of two numbers for label style (size, boldness), default is c(2, 1)

axis_style

Vector of two numbers for axis style (size, boldness), default is c(2, 1)

title_style

Vector of two numbers for title style (size, boldness), default is c(2.5, 2)

...

Additional parameters passed to plot functions

Examples

# colocboost example
set.seed(1)
N <- 1000
P <- 100
# Generate X with LD structure
sigma <- 0.9^abs(outer(1:P, 1:P, "-"))
X <- MASS::mvrnorm(N, rep(0, P), sigma)
colnames(X) <- paste0("SNP", 1:P)
L <- 3
true_beta <- matrix(0, P, L)
true_beta[10, 1] <- 0.5 # SNP10 affects trait 1
true_beta[10, 2] <- 0.4 # SNP10 also affects trait 2 (colocalized)
true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
Y <- matrix(0, N, L)
for (l in 1:L) {
  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1)
}
res <- colocboost(X = X, Y = Y)
colocboost_plot(res, plot_cols = 1)
colocboost_plot(res, plot_cols = 1, outcome_idx = 1:3)