mvsusie_plot | R Documentation |
Create the PIP plot and accompanying effect plot showing the effect estimates and significance of the effects for all the traits. A z-scores plot is also created when z-scores are available.
mvsusie_plot(
fit,
chr = 1,
pos = seq(1, length(fit$variable_names)),
markers = fit$variable_names,
conditions = fit$condition_names,
poslim = range(pos),
lfsr_cutoff = 0.01,
sentinel_only = TRUE,
cs_plot = names(fit$sets$cs),
add_cs = FALSE,
conditional_effect = TRUE,
cs_colors = c("#1f78b4", "#33a02c", "#e31a1c", "#ff7f00", "#6a3d9a", "#b15928",
"#a6cee3", "#b2df8a", "#fb9a99", "#fdbf6f", "#cab2d6", "#ffff99", "gray", "cyan")
)
fit |
The mvSuSiE fitted model. |
chr |
The chromosome number. |
pos |
The positions of the genetic markers. It should have the
same length as |
markers |
The names of the genetic markers (usually SNPs). |
conditions |
The names of the conditions. |
poslim |
The range of positions to show in the PIP plot. |
lfsr_cutoff |
The significance level for lfsr. The default is 0.01. |
sentinel_only |
If |
cs_plot |
The CSs included in the plot. The default is to show all CSs. |
add_cs |
If |
conditional_effect |
If |
cs_colors |
The color palette for CSs. |
The output includes the PIP plot, effect plot, z-scores
plot (if z-scores are available in fit
), and the table of
effect estimates at sentinel markers.
# See the "mvsusie_intro" vignette for examples.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.