Commit 9aee6225 authored by Kosmas Hench's avatar Kosmas Hench
Browse files

update figures and documentation

parent 5b2f663f

0_data/0_scripts/S02.functions.R

+23 −23
Original line number Diff line number Diff line
@@ -88,8 +88,8 @@ plot_fun <- function(data,loc,sel,gl){ 
                            '18175','18176',bold('18178'),'18179',bold('18180'),'18163','18261',bold('18267'),

                            bold('18274'),bold('18276'),'19881','20092','20120','20126','20128','20135','20149'),

             hon=expression('20599','20600','20601','20602','20603','20604','20605','20606','20607','20608',

                            '20609','20610','20551','20552','20553',bold('20554'),'20555','20556',

                            bold('20558'),bold('20559'),'20625',bold('20633'),'20635','20638','20560',

                            '20609','20610','20551','20552','20553','20554','20555','20556',

                            bold('20558'),'20559','20625',bold('20633'),'20635','20638','20560',

                            '20561','20562','20563','20564','20565','20566','20567','20568','20571','20572'),

             boc=expression("16_21-30","18418","18424","18428","18436","18901","18902","18903",

                            "18904","18905","18906","18907","18909","18419","18421","18422",

0_data/0_scripts/subsetSNPs_byFST.R

+2 −2
Original line number Diff line number Diff line
@@ -14,12 +14,12 @@ filter1000snps <- function(name){ 
  mutate(FST_RANK = rank(-WEIR_AND_COCKERHAM_FST,ties.method = "random")) %>%

  select(CHROM,POS,WEIR_AND_COCKERHAM_FST,FST_RANK)



  filterSet <- raw %>% filter(FST_RANK < 1001)

  filterSet <- raw %>% filter(FST_RANK < 801)



  h <- hist(filterSet$WEIR_AND_COCKERHAM_FST)

  print(min(filterSet$WEIR_AND_COCKERHAM_FST))



  write.table(filterSet %>% select(CHROM,POS),paste0(args[7],'2_output/08_popGen/11_newHyb/snpSets/filterSet.1k.',name,'.snps'),

  write.table(filterSet %>% select(CHROM,POS),paste0(args[7],'2_output/08_popGen/11_newHyb/snpSets/filterSet.80SNPs.',name,'.snps'),

            sep = '\t',row.names = F,quote = F)

  return(h)

  }

2_reSeq-scripts/2-2_popGen/00_templates/2.2.11.2.fasteprr_step2_temp.sh

+1 −1
Original line number Diff line number Diff line
@@ -12,4 +12,4 @@ cd $WORK/2_output/08_popGen/12_fasteprr 
mkdir -p step2

mkdir -p step2/XXnameXX



Rscript --vanilla $WORK/0_data/0_scripts/fasteprr_step2_single.R $PWD step1 step2 XXnameXX
 
Rscript --vanilla $WORK/0_data/0_scripts/fasteprr_step2.R $PWD step1 step2 XXnameXX