modifs mark_estmap for first/last groups

.Rproj.user/9DAE6990/pcs/workbench-pane.pper

 {
-    "TabSet1" : 1,
+    "TabSet1" : 0,
     "TabSet2" : 0,
     "TabZoom" : {
     }

.Rproj.user/9DAE6990/persistent-state

 build-last-errors="[]"
 build-last-errors-base-dir="~/Documents/PhD/stuart_package/stuart/"
-build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source stuart\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’\\n\",\"type\":1},{\"output\":\"* installing *source* package ‘stuart’ ...\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** moving datasets to lazyload DB\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (stuart)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
+build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source stuart\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing *source* package ‘stuart’ ...\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** moving datasets to lazyload DB\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (stuart)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
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-imageDirtyState="0"
+imageDirtyState="1"
 saveActionState="0"

.Rproj.user/shared/notebooks/paths

+/Users/mariebourdon/Documents/PhD/stuart_package/stuart/DESCRIPTION="5140B408"
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/geno_strains.R="EBA82473"
+/Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/mark_allele.R="A0A182D3"
+/Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/mark_estmap.R="57E1825F"
+/Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/mark_match.R="FFA1BE52"
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/mark_prop.R="30FA9E8C"
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/tab_mark.R="F0B2417"
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/R/write_rqtl.R="F07CE16C"

R/mark_estmap.R

@@ -87,12 +87,17 @@ mark_estmap <- function(tab,map,annot,d=20,r=10,n=5){
                                                     T ~ group))
       new_pos <- match("new",tab_chr$group)
       g <- g+1
-
     }
     tab_chr <- tab_chr %>% tidyr::fill(group)
     tab_chr <- tab_chr %>% mutate(group=as.numeric(group)) %>% select(-row)
-    summa <- tab_chr %>% group_by(group) %>% summarise(n=n())
-    gremove <- summa %>% filter(n<10) %>% select(group) %>% pull()
+    summa <- tab_chr %>% group_by(group) %>% summarise(N=n())
+    summa <- summa %>% mutate(n_bef=lag(N,default=9))
+    summa <- summa %>% mutate(n_af=lead(N,default=9))
+    summa <- summa %>% mutate(excl=case_when(N<n ~ 1,
+                                             T ~ 0))
+    summa <- summa %>% mutate(ex_bef=lag(excl,default=9))
+    summa <- summa %>% mutate(ex_af=lead(excl,default=9))
+    gremove <- summa %>% filter(excl==1 & ((ex_bef!=1 & ex_af!=1) | (ex_bef!=9 & ex_af!=9))) %>% select(group) %>% pull()
     mark_remove <- bind_rows(mark_remove,tab_chr %>% filter(group %in% gremove))
   }
 

article/article_figures.Rmd

@@ -361,7 +361,7 @@ plotmap_after <- ~plotMap(cross_after,newmap_after,shift=TRUE,main="After stuart
 
 ```{r after_estmap}
 #filter with mark_estmap
-tab2 <- mark_estmap(tab2,newmap_after)
+tab2 <- mark_estmap(tab2,newmap_after,annot_mini)
 
 # create rqtl csv file
 write_rqtl(geno=genos,pheno=phenos,tab=tab2,ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox",path="files/cluster2/cross_after.csv")

article/files/cluster2/after.out

  --Read the following data:
 	 176  individuals
-	 2236  markers
+	 2235  markers
 	 4  phenotypes
  --Cross type: f2 

article/tables/tab_alleles.tex

 % latex table generated in R 4.0.4 by xtable 1.8-4 package
-% Mon Jan  3 17:04:48 2022
+% Tue Jan  4 10:53:15 2022
 \begin{table}[ht]
 \centering
 \begin{tabular}{lllllrrr}