Commit cbc7183d authored by Kosmas Hench's avatar Kosmas Hench
Browse files

correct S10 and S11

parent c97fc920

3_figures/F_scripts/Rplots.pdf

(3.53 KiB)

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3_figures/F_scripts/S10.R

+1 −1
Original line number Original line Diff line number Diff line
@@ -15,7 +15,7 @@ karyo <- read.csv('../../0_data/0_resources/F2.karyo.txt',sep='\t') %>% 
bh <- read.csv('../../2_output/08_popGen/05_fst/bel-hon.50kb.5kb.windowed.weir.fst',sep='\t') %>%

bh <- read.csv('../../2_output/08_popGen/05_fst/bel-hon.50kb.5kb.windowed.weir.fst',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');





bp <- read.csv('../../2_output/08_popGen/05_fst/bel-hon.50kb.5kb.windowed.weir.fst',sep='\t') %>%

bp <- read.csv('../../2_output/08_popGen/05_fst/bel-boc.50kb.5kb.windowed.weir.fst',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');





hp <- read.csv('../../2_output/08_popGen/05_fst/hon-boc.50kb.5kb.windowed.weir.fst',sep='\t') %>%

hp <- read.csv('../../2_output/08_popGen/05_fst/hon-boc.50kb.5kb.windowed.weir.fst',sep='\t') %>%

3_figures/F_scripts/S11.R

+1 −1
Original line number Original line Diff line number Diff line
@@ -15,7 +15,7 @@ karyo <- read.csv('../../0_data/0_resources/F2.karyo.txt',sep='\t') %>% 
bh <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-hon-gemma.lm.50k.5k.smooth',sep='\t') %>%

bh <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-hon-gemma.lm.50k.5k.smooth',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');





bp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-hon-gemma.lm.50k.5k.smooth',sep='\t') %>%

bp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-boc-gemma.lm.50k.5k.smooth',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');





hp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/hon-boc-gemma.lm.50k.5k.smooth',sep='\t') %>%

hp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/hon-boc-gemma.lm.50k.5k.smooth',sep='\t') %>%

3_figures/S10.Rmd

+21 −21
Original line number Original line Diff line number Diff line
@@ -83,7 +83,7 @@ karyo <- read.csv('../../0_data/0_resources/F2.karyo.txt',sep='\t') %>% 
bh <- read.csv('../../2_output/08_popGen/05_fst/bel-hon.50kb.5kb.windowed.weir.fst',sep='\t') %>%

bh <- read.csv('../../2_output/08_popGen/05_fst/bel-hon.50kb.5kb.windowed.weir.fst',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');





bp <- read.csv('../../2_output/08_popGen/05_fst/bel-hon.50kb.5kb.windowed.weir.fst',sep='\t') %>% 

bp <- read.csv('../../2_output/08_popGen/05_fst/bel-boc.50kb.5kb.windowed.weir.fst',sep='\t') %>% 

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');





hp <- read.csv('../../2_output/08_popGen/05_fst/hon-boc.50kb.5kb.windowed.weir.fst',sep='\t') %>%

hp <- read.csv('../../2_output/08_popGen/05_fst/hon-boc.50kb.5kb.windowed.weir.fst',sep='\t') %>%

3_figures/S11.Rmd

+20 −20
Original line number Original line Diff line number Diff line
@@ -48,7 +48,7 @@ karyo <- read.csv('../../0_data/0_resources/F2.karyo.txt',sep='\t') %>% 
bh <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-hon-gemma.lm.50k.5k.smooth',sep='\t') %>%

bh <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-hon-gemma.lm.50k.5k.smooth',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BH',RUN='BH');





bp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-hon-gemma.lm.50k.5k.smooth',sep='\t') %>% 

bp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/bel-boc-gemma.lm.50k.5k.smooth',sep='\t') %>%

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');

  merge(.,(karyo %>% select(-GEND,-GROUP)),by='CHROM',allx=T) %>% mutate(POS=(BIN_START+BIN_END)/2,GPOS=POS+GSTART,COL='BP',RUN='BP');





hp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/hon-boc-gemma.lm.50k.5k.smooth',sep='\t') %>%

hp <- read.csv('../../2_output/08_popGen/06_GxP/smoothed/50kb/hon-boc-gemma.lm.50k.5k.smooth',sep='\t') %>%