Sweep Plots

sweep_details.R

library(tidyverse)

sweep_detail_plot <- function(scaffold,xl,rl,gff,sf2_data){

  anno_data <- gff %>% 
    filter(seqid==scaffold) %>% 
    mutate(geneid=str_extract(attributes,"m[^\\;]+"))

  anno_data$type <- factor(anno_data$type)

  ggplot(sf2_data,aes(x=location/1000000,y=LR)) + 
  geom_point() +
  xlim(xl/1000000,rl/1000000)  +
  geom_segment(data=anno_data %>% filter(type=="gene"),size=3,aes(color=type,x=start/1e6,xend=end/1e6,y=-(10*as.numeric(type)+20),yend=-(10*as.numeric(type)+20))) + guides(fill=FALSE) +
  theme_minimal() + xlab("Position Mb") + theme(legend.title = element_blank()) + theme(text= element_text(size=16))
}

aten_gff <- read_tsv("aten_0.1.maker_post_001.genes.gff",
                     col_names = c("seqid","source","type","start","end","score","strand","phase","attributes"))

sf2_data <- read_table2("sweepfinderdata.sf2")

sweep_detail_plot("sc0000029",xl=2.8e6,rl=3e6,aten_gff,sf2_data)