susie_plot {susieR} | R Documentation |
SuSiE Plots.
Description
susie_plot
produces a per-variable summary of
the SuSiE credible sets. susie_plot_iteration
produces a
diagnostic plot for the susie model fitting. For
susie_plot_iteration
, several plots will be created if
track_fit = TRUE
when calling susie
.
Usage
susie_plot(
model,
y,
add_bar = FALSE,
pos = NULL,
b = NULL,
max_cs = 400,
add_legend = NULL,
...
)
susie_plot_iteration(model, L, file_prefix, pos = NULL)
Arguments
model |
A SuSiE fit, typically an output from
|
y |
A string indicating what to plot: either |
add_bar |
If |
pos |
Indices of variables to plot. If |
b |
For simulated data, set |
max_cs |
The largest credible set to display, either based on
purity (set |
add_legend |
If |
... |
Additional arguments passed to
|
L |
An integer specifying the number of credible sets to plot. |
file_prefix |
Prefix to path of output plot file. If not
specified, the plot, or plots, will be saved to a temporary
directory generated using |
Value
Invisibly returns NULL
.
See Also
Examples
set.seed(1)
n = 1000
p = 1000
beta = rep(0,p)
beta[sample(1:1000,4)] = 1
X = matrix(rnorm(n*p),nrow = n,ncol = p)
X = scale(X,center = TRUE,scale = TRUE)
y = drop(X %*% beta + rnorm(n))
res = susie(X,y,L = 10)
susie_plot(res,"PIP")
susie_plot(res,"PIP",add_bar = TRUE)
susie_plot(res,"PIP",add_legend = TRUE)
susie_plot(res,"PIP", pos=1:500, add_legend = TRUE)
# Plot selected regions with adjusted x-axis position label
res$genomic_position = 1000 + (1:length(res$pip))
susie_plot(res,"PIP",add_legend = TRUE,
pos = list(attr = "genomic_position",start = 1000,end = 1500))
# True effects are shown in red.
susie_plot(res,"PIP",b = beta,add_legend = TRUE)
set.seed(1)
n = 1000
p = 1000
beta = rep(0,p)
beta[sample(1:1000,4)] = 1
X = matrix(rnorm(n*p),nrow = n,ncol = p)
X = scale(X,center = TRUE,scale = TRUE)
y = drop(X %*% beta + rnorm(n))
res = susie(X,y,L = 10)
susie_plot_iteration(res, L=10)