Commit 5b2f663f authored by Kosmas Hench's avatar Kosmas Hench
Browse files

include fasteprr

parent 7df22ce7

0_data/0_scripts/S14.functions.R→0_data/0_scripts/E1.functions.R

+8 −3
Original line number Diff line number Diff line 
get_anno_df_single_line <- function(searchLG,gfffile,

                                    xrange,

                                    anno_rown=4){

                                    genes_of_interest,

                                    genes_of_sec_interest,

                                    anno_rown=3){

  gff_filter <- list(seqid=searchLG)

  data <- as.data.frame(readGFF(gfffile,filter=gff_filter)) %>% mutate(Parent=as.character(Parent))#%>%

  #rowwise() %>% mutate(Parent=ifelse(length(Parent)==0,ID,Parent))
@@ -13,13 +15,16 @@ get_anno_df_single_line <- function(searchLG,gfffile, 
           pe=ifelse(strand=='-',checkStart,checkEnd),

           labelx=mean(c(sort(c(xrange[1],ps))[2],

                         sort(c(xrange[2],pe))[1])),

           window='bold(Gene)') %>% 

           window='bold(Gene)',

           clr=ifelse(Parentgenename %in% genes_of_interest,"y",

                      ifelse(Parentgenename %in% genes_of_sec_interest,"z","x"))) %>% 

    select(-Parent);

  names(mRNAs)[names(mRNAs)=='ID'] <- 'Parent'

  

  exons <- data %>% filter(type=='exon',end>xrange[1],start<xrange[2]) %>% 

    merge(.,mRNAs %>% select(Parent,yl),by='Parent',all.x=T) %>% 

    merge(.,mRNAs %>% select(Parent,yl,clr),by='Parent',all.x=T) %>% 

    mutate(ps=ifelse(strand=='-',end,start),

           pe=ifelse(strand=='-',start,end),

           window='bold(Gene)')

  return(list(mRNAs,exons))}

0_data/0_scripts/F3.plot_fun.R→0_data/0_scripts/E1.plot_fun.R

+27 −27
Original line number Diff line number Diff line 
create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchsnp,muskID){

  source('../../0_data/0_scripts/F3.functions.R');

  source('../../0_data/0_scripts/F3.getFSTs.R')

  source('../../0_data/0_scripts/F3.getGxP.R')

  source('../../0_data/0_scripts/F3.getDXY.R')

  source('../../0_data/0_scripts/E1.functions.R');

  source('../../0_data/0_scripts/E1.getFSTs.R')

  source('../../0_data/0_scripts/E1.getGxP.R')

  source('../../0_data/0_scripts/E1.getDXY.R')



  highclr <- '#3bb33b'

  theme_set(theme_minimal(base_size = 6))
@@ -90,7 +90,7 @@ create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchs 
 if(muskID=='A'){

   p11$layers[[4]]$data$label <- c("italic(sox10)","italic(rnaseh2a)")

 } else if(muskID=='B'){

     p11$layers[[4]]$data$label <- c("italic(casz1^3)","italic(casz1^2)","italic(casz1^1)")

     p11$layers[[4]]$data$label <- c("italic(casz1.3)","italic(casz1.2)","italic(casz1.1)")

   } else if(muskID=='C'){

     p11$layers[[4]]$data$label <- c('italic(hoxc10a)',"italic(hoxc11a)","italic(hoxc12a)","italic(hoxc13a)","italic(calcoco1)")

   }else if(muskID=='E'){