diff --git a/_pkgdown.yml b/_pkgdown.yml index ca0dea6..b180b8c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -36,6 +36,7 @@ articles: desc: "Advanced topics and special cases in colocalization and fine-mapping analysis." contents: - Partial_Overlap_Variants + - ColocBoost_Update - ColocBoost_Wrapper_Pipeline - LD_Free_Colocalization - Ambiguous_Colocalization diff --git a/man/figures/ColocBoost_update.gif b/man/figures/ColocBoost_update.gif new file mode 100644 index 0000000..bb54393 Binary files /dev/null and b/man/figures/ColocBoost_update.gif differ diff --git a/vignettes/ColocBoost_Update.Rmd b/vignettes/ColocBoost_Update.Rmd new file mode 100644 index 0000000..a7de526 --- /dev/null +++ b/vignettes/ColocBoost_Update.Rmd @@ -0,0 +1,33 @@ +--- +title: "Animation Example: Proximity Gradient Boosting Algorithm" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Animation Example: Proximity Gradient Boosting Algorithm} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + + + +This vignette visualizes the iterative process of proximity gradient boosting proposed in ColocBoost from an extensive simulation example. + + +- **Red point**: the standard gradient boosting update for only the best single-effect variant $j_k^*$ in each iteration. +- **Blue points**: the proximity gradient boosting update, where it probabilistically incorporates the LD proxies of $j_k^*$ by applying a convex relaxation to the gradient. + +The animation below demonstrates how ColocBoost iteratively updates across multiple rounds. +Observe how the blue points (proxies) distribute around the selected best update, showing the algorithm's ability to capture LD structure during optimization. + +```{r, out.width="80%"} +knitr::include_graphics("../man/figures/ColocBoost_update.gif") +``` + + +See more details in the [ColocBoost Manuscript](https://www.medrxiv.org/content/10.1101/2025.04.17.25326042v1) and the [GitHub repository](https://github.com/StatFunGen/colocboost). \ No newline at end of file