test.Rmd

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output: pdf_document
geometry: margin=1in
mainfont: Times New Roman
---

```{r,fig.width=7.5, fig.height=7.5,warning=F, message=F, echo=F,comment="K",results='asis'}

library(cegwas)
library(cegwas)
library(genetics)
library(pander)
library(dplyr)
library(ggplot2)
library(data.table)
library(grid)
library(stringr)
library(gridExtra)
library(knitr)
library(tidyr)
library(scales)
library(gtable)
library(cowplot)

setwd("/Users/kristen/Documents/transposon_figure_data/data")
#load("Processed_Transposon_Mappings_2.Rda")
#load("Processed_Transposon_Mappings_SUBSET.Rda")
load("Processed_Transposon_Mappings_SUBSET2.Rda")


for (i in unique(processed_mapping_df$trait)){
  test<-filter(processed_mapping_df,trait==i)
  sns <- dplyr::filter(test, aboveBF == 1, !is.na(peak_id) )
  #ans<-
  
  if (nrow(sns)>1){
  crs <- plot_peak_ld(sns)
  #ld<-ggplotGrob(crs)
  plot(crs)

  } else {
  crs<-NULL #single peak, no need to check for LD
  }


}