Commit e4900339 authored by Kosmas Hench's avatar Kosmas Hench
Browse files

update figures

parent 8ec8eaab

0_data/0_img/legend-pw-single-cairo.svg

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0_data/0_img/legend-pw-single.ps

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0_data/0_img/legend-pw-single.ps.pdf

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0_data/0_scripts/F3.plot_fun.R

+7 −5
Original line number Diff line number Diff line
@@ -32,7 +32,8 @@ create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchs 
  

  clr <- c('#fb8620','#1b519c','#d93327')

  annoclr <- c('lightgray',highclr,rgb(.3,.3,.3))[1:3]

  df_list[[1]] <- df_list[[1]] %>% mutate(label=paste("italic(",tolower(Parentgenename),")",sep='') )

  df_list[[1]] <- df_list[[1]] %>% 

    mutate(label=paste("italic(",tolower(Parentgenename),")",sep='') )

  

  LW <- .3;lS <- 9;tS <- 6

  plotSET <-  theme(rect = element_blank(),
@@ -67,7 +68,7 @@ create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchs 
    # color settings

    scale_color_manual(values=annoclr,breaks=c("x","y","z"),guide=F)+  

    scale_fill_manual(values=annoclr,guide=F)+

    scale_x_continuous(name=paste(searchLG,' (',muskID,', kb)'),expand=c(0,0),position = 'top')+

    scale_x_continuous(name=paste0(searchLG,' (',muskID,', kb)'),expand=c(0,0),position = 'top')+

    scale_y_continuous(breaks = seq(0,.75,length.out = 4))+

    theme(rect = element_blank(),

          text=element_text(size=tS,color='black'),
@@ -130,7 +131,8 @@ create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchs 
              ,aes(x=POS,y=avgp_wald,col=run),lwd=LW)+

    # geom_line(data=(data_pfst_pw %>% filter(POS > xr[1],POS<xr[2]))

    #            ,aes(x=POS,y=avgp_wald,col=run,linetype=group),lwd=1)+

    scale_color_manual(values=c(clr,annoclr),breaks=c("nig-pue","nig-uni","pue-uni","x","y","z"),guide=F)+  

    scale_color_manual(values=c(clr,annoclr),

                       breaks=c("nig-pue","nig-uni","pue-uni","x","y","z"),guide=F)+  

    facet_grid(window~.,scales='free_y',

               switch = 'y',labeller = label_parsed,as.table = T)+

    scale_x_continuous(name=searchLG,expand=c(0,0),position = 'top')+
@@ -151,7 +153,7 @@ create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchs 
    scale_linetype(name='location',label=c('Belize','Honduras','Panama'))+

    guides(linetype= guide_legend(override.aes = list(color = 'black')))+plotSET

  

  

  p2 <- plot_grid(p11,p12,p13,p14,

                  ncol = 1,align = 'v',axis = 'r',rel_heights = c(1.3,rep(1,3)))

                  ncol = 1,align = 'v',axis = 'r',

                  rel_heights = c(1.3,rep(1,3)))

  return(p2)}
 
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0_data/0_scripts/F4.genomeWide_box.R

+1 −1
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@@ -34,7 +34,7 @@ pBOX <- ggplot(BW,aes(x=run,y=R.2))+ 
  geom_point(inherit.aes = F, data=dt2,aes(x=run,y=val,fill=type),shape=23,size=1)+

  scale_x_discrete(labels = expression(Global,Panama,Belize,Honduas,

                                       italic("H. nigricans"),italic("H. puella"),italic("H. unicolor")))+

  scale_y_continuous('genome wide r²')+

  scale_y_continuous('genome wide ILD (r²)')+

  scale_fill_manual('',values = clr[c(6,1)],labels=c('mean','median'))+

  guides(shape = guide_legend(ncol = 1))+

  theme(legend.position = c(-.4,1.27),