From 776b1456533a41bfbdae72e21b0e164c0cd809c1 Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 07:51:00 -0600
Subject: [PATCH 1/9] Create plot_progeny_dosage_change.R

---
 R/plot_progeny_dosage_change.R | 150 +++++++++++++++++++++++++++++++++
 1 file changed, 150 insertions(+)
 create mode 100644 R/plot_progeny_dosage_change.R

diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
new file mode 100644
index 00000000..202546e5
--- /dev/null
+++ b/R/plot_progeny_dosage_change.R
@@ -0,0 +1,150 @@
+#############################################################################################################################
+#' Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error
+#'
+#' Outputs a graphical representation ggplot with the percent of data changed
+#'
+#' @param map_list a list of multiple \code{mappoly.map.list}
+#'
+#' @param error error rate used in global error in the `calc_genoprob_error()`
+#'
+#' 
+#'
+#' @return A ggplot of the changed and imputed genotypic dosages
+#'
+#' @examples
+#'     all.mrk <- make_seq_mappoly(hexafake, 'all')
+#'     seq1.mrk <- make_seq_mappoly(hexafake, 'seq1')
+#'     plot(seq1.mrk)
+#'     some.mrk.pos <- c(1,4,28,32,45)
+#'     (some.mrk.1 <- make_seq_mappoly(hexafake, some.mrk.pos))
+#'     plot(some.mrk.1)
+#'
+#' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
+#'
+#' @import ggplot2, reshape
+#' @export plot_progeny_dosage_change
+
+plot_progeny_dosage_change <- function(map_list, error){
+  map=map_list
+  if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here")
+  
+  dat <- get(map[[1]]$info$data.name)
+  ploidy <- map[[1]]$info$ploidy
+  
+  print("calculating genoprob error")
+  
+  genoprob  <- vector("list", 7)
+  for(i in 1:7){
+    genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, verbose = F)
+  }
+  
+  print("calculating homologprob")
+  
+  homoprobs = calc_homologprob(genoprob, verbose=F)
+  
+  print("comparing to orginal")
+  
+  P=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$P), recursive=F)
+  Q=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$Q), recursive=F)
+  
+  
+  
+  P_matrix=matrix(0,nrow=length(P),ncol=ploidy)
+  Q_matrix=matrix(0,nrow=length(Q),ncol=ploidy)
+  #colnames(P_matrix)=c("a","b","c","d")
+  #colnames(Q_matrix)=c("e","f","g","h")
+  
+  
+  for(i in 1:nrow(P_matrix)){
+    P_matrix[i,unlist(P[i])]=1
+  }
+  
+  for(i in 1:nrow(Q_matrix)){
+    Q_matrix[i,unlist(Q[i])]=1
+  }
+  
+  mrks_mapped=unlist(lapply(map, function(x) x$info$mrk.names) )
+  
+  PQ_matrix=cbind(P_matrix,Q_matrix)
+  rownames(PQ_matrix)=mrks_mapped
+  colnames(PQ_matrix)=c(letters[1:(ploidy*2)])
+  
+  
+  homoprob=homoprobs$homoprob
+  inds = unique(homoprob$individual)
+  mrks = unique(homoprob$marker)
+  
+  
+  
+  temp = matrix(NA,length(mrks),length(inds))
+  rownames(temp)=mrks
+  colnames(temp)=inds
+  
+  
+  homoprob=as.matrix(homoprob)
+  
+  
+  
+  homoprob_ind <- split.data.frame(homoprob, homoprob[,3])
+  
+  test <- sapply(homoprob_ind, function(x) {
+    by_marker <- split.data.frame(x, x[,1]) 
+    final_matrix <- t(sapply(by_marker, function(y) y[order(y[,4], decreasing = T),][1:4,2]))
+    final_vector <- apply(final_matrix, 1, function(w) paste0(w, collapse = ""))
+    return(final_vector)
+  })
+  
+  
+  
+  test=test[,order(colnames(test))]
+  test=test[match(mrks,rownames(test)),]
+  
+  finished = test
+
+  
+  
+  for(a in 1:length(mrks)){
+    for(b in 1:length(inds)){
+      finished[a,b]=sum(PQ_matrix[a,substr(test[a,b], 1,1)],
+                        PQ_matrix[a,substr(test[a,b], 2,2)],
+                        PQ_matrix[a,substr(test[a,b], 3,3)],
+                        PQ_matrix[a,substr(test[a,b], 4,4)])
+      
+    }
+    #print(a)
+  }
+  
+  
+  
+  original_geno=as.matrix(dat$geno.dose[which(rownames(dat$geno.dose)%in%mrks),])
+  original_geno=original_geno[,order(colnames(original_geno))]
+  identical(colnames(finished), colnames(original_geno))
+  
+  identical(original_geno, finished)
+  which(!original_geno==finished)
+  original_geno[which(!original_geno==finished)]
+  
+  
+  percent_imputed=length(which(!original_geno==finished&original_geno==5))/length(original_geno)*100
+  percent_changed=length(which(!original_geno==finished&!original_geno==5))/length(original_geno)*100
+  
+  
+  
+  
+  colors = c("red","chartreuse","black")
+  empty_matrix=matrix(0,nrow(original_geno),ncol(original_geno))
+  empty_matrix[which(original_geno==finished)]="unchanged"
+  empty_matrix[which(!original_geno==finished&original_geno==5)]="imputed"
+  empty_matrix[which(!original_geno==finished&!original_geno==5)]="changed"
+  empty_matrix_melt=melt(empty_matrix)
+  plot1<-ggplot(empty_matrix_melt, aes(X1, X2, fill= factor(value))) + 
+    geom_tile()+scale_fill_manual(values=colors)+
+    xlab("Markers")+
+    ylab("Individuals")+
+    ggtitle(paste0("changed = ",round(percent_changed, digits=3),"% ","imputed = ", round(percent_imputed, digits=3),"%"))
+  
+  print("done")
+  
+  return(plot1) 
+  
+}
\ No newline at end of file

From aff074ea8f68ec93a40a9bbb876a42b170013d0b Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 07:59:30 -0600
Subject: [PATCH 2/9] Update plot_progeny_dosage_change.R

---
 R/plot_progeny_dosage_change.R | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index 202546e5..7795dfdd 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -1,4 +1,3 @@
-#############################################################################################################################
 #' Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error
 #'
 #' Outputs a graphical representation ggplot with the percent of data changed
@@ -12,12 +11,7 @@
 #' @return A ggplot of the changed and imputed genotypic dosages
 #'
 #' @examples
-#'     all.mrk <- make_seq_mappoly(hexafake, 'all')
-#'     seq1.mrk <- make_seq_mappoly(hexafake, 'seq1')
-#'     plot(seq1.mrk)
-#'     some.mrk.pos <- c(1,4,28,32,45)
-#'     (some.mrk.1 <- make_seq_mappoly(hexafake, some.mrk.pos))
-#'     plot(some.mrk.1)
+
 #'
 #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
 #'

From 5518748f36d96a897245a1875a8e9dc8d7b91c08 Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 08:10:16 -0600
Subject: [PATCH 3/9] documentation

---
 NAMESPACE                         |  3 +++
 R/plot_progeny_dosage_change.R    |  2 +-
 man/plot_progeny_dosage_change.Rd | 26 ++++++++++++++++++++++++++
 3 files changed, 30 insertions(+), 1 deletion(-)
 create mode 100644 man/plot_progeny_dosage_change.Rd

diff --git a/NAMESPACE b/NAMESPACE
index d652533f..d225a1f1 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -114,6 +114,7 @@ export(plot_compare_haplotypes)
 export(plot_genome_vs_map)
 export(plot_map_list)
 export(plot_mrk_info)
+export(plot_progeny_dosage_change)
 export(poly_cross_simulate)
 export(print_mrk)
 export(read_fitpoly)
@@ -135,10 +136,12 @@ export(table_to_mappoly)
 export(update_map)
 export(update_missing)
 export(v_2_m)
+import("ggplot2,")
 import(RCurl)
 import(Rcpp)
 import(fields)
 import(parallel)
+import(reshape)
 importFrom(Rcpp,sourceCpp)
 importFrom(RcppParallel,RcppParallelLibs)
 importFrom(cli,rule)
diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index 7795dfdd..238489a0 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -11,7 +11,7 @@
 #' @return A ggplot of the changed and imputed genotypic dosages
 #'
 #' @examples
-
+#'     plot_progeny_dosage_change(map_list=MAPs, error=0.05)
 #'
 #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
 #'
diff --git a/man/plot_progeny_dosage_change.Rd b/man/plot_progeny_dosage_change.Rd
new file mode 100644
index 00000000..4b6c3f0a
--- /dev/null
+++ b/man/plot_progeny_dosage_change.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_progeny_dosage_change.R
+\name{plot_progeny_dosage_change}
+\alias{plot_progeny_dosage_change}
+\title{Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error}
+\usage{
+plot_progeny_dosage_change(map_list, error)
+}
+\arguments{
+\item{map_list}{a list of multiple \code{mappoly.map.list}}
+
+\item{error}{error rate used in global error in the `calc_genoprob_error()`}
+}
+\value{
+A ggplot of the changed and imputed genotypic dosages
+}
+\description{
+Outputs a graphical representation ggplot with the percent of data changed
+}
+\examples{
+    plot_progeny_dosage_change(map_list=MAPs, error=0.05)
+
+}
+\author{
+Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
+}

From 31658345bb9f57afa41d91fa7473c761dffc45dc Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 08:38:18 -0600
Subject: [PATCH 4/9] documentation1

---
 NAMESPACE                      | 2 +-
 R/plot_progeny_dosage_change.R | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index d225a1f1..4033059c 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -136,10 +136,10 @@ export(table_to_mappoly)
 export(update_map)
 export(update_missing)
 export(v_2_m)
-import("ggplot2,")
 import(RCurl)
 import(Rcpp)
 import(fields)
+import(ggplot2)
 import(parallel)
 import(reshape)
 importFrom(Rcpp,sourceCpp)
diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index 238489a0..67dc708e 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -15,7 +15,8 @@
 #'
 #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
 #'
-#' @import ggplot2, reshape
+#' @import ggplot2 
+#' @import reshape
 #' @export plot_progeny_dosage_change
 
 plot_progeny_dosage_change <- function(map_list, error){

From 09df93f977a194208f55e560f8cd695f85677372 Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 11:37:35 -0600
Subject: [PATCH 5/9] Update plot_progeny_dosage_change.R

fixed reshape2 dependency code
---
 R/plot_progeny_dosage_change.R | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index 67dc708e..a9ba2f32 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -5,7 +5,7 @@
 #' @param map_list a list of multiple \code{mappoly.map.list}
 #'
 #' @param error error rate used in global error in the `calc_genoprob_error()`
-#'
+#' @param verbose T or F for `calc_genoprob_error()` and `calc_homologprob()`
 #' 
 #'
 #' @return A ggplot of the changed and imputed genotypic dosages
@@ -16,10 +16,10 @@
 #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
 #'
 #' @import ggplot2 
-#' @import reshape
+#' @import reshape2
 #' @export plot_progeny_dosage_change
 
-plot_progeny_dosage_change <- function(map_list, error){
+plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   map=map_list
   if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here")
   
@@ -30,12 +30,12 @@ plot_progeny_dosage_change <- function(map_list, error){
   
   genoprob  <- vector("list", 7)
   for(i in 1:7){
-    genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, verbose = F)
+    genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, verbose = verbose)
   }
   
   print("calculating homologprob")
   
-  homoprobs = calc_homologprob(genoprob, verbose=F)
+  homoprobs = calc_homologprob(genoprob, verbose=verbose)
   
   print("comparing to orginal")
   
@@ -132,7 +132,7 @@ plot_progeny_dosage_change <- function(map_list, error){
   empty_matrix[which(!original_geno==finished&original_geno==5)]="imputed"
   empty_matrix[which(!original_geno==finished&!original_geno==5)]="changed"
   empty_matrix_melt=melt(empty_matrix)
-  plot1<-ggplot(empty_matrix_melt, aes(X1, X2, fill= factor(value))) + 
+  plot1<-ggplot(empty_matrix_melt, aes(Var1, Var2, fill= factor(value))) + 
     geom_tile()+scale_fill_manual(values=colors)+
     xlab("Markers")+
     ylab("Individuals")+
@@ -142,4 +142,6 @@ plot_progeny_dosage_change <- function(map_list, error){
   
   return(plot1) 
   
-}
\ No newline at end of file
+}
+
+str(empty_matrix)

From 34769ecaedd7cb4661661acb17c796f7b2959e42 Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 11:47:41 -0600
Subject: [PATCH 6/9] update documentation

---
 NAMESPACE                         | 2 +-
 man/plot_progeny_dosage_change.Rd | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 4033059c..8dbb11a3 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -141,7 +141,7 @@ import(Rcpp)
 import(fields)
 import(ggplot2)
 import(parallel)
-import(reshape)
+import(reshape2)
 importFrom(Rcpp,sourceCpp)
 importFrom(RcppParallel,RcppParallelLibs)
 importFrom(cli,rule)
diff --git a/man/plot_progeny_dosage_change.Rd b/man/plot_progeny_dosage_change.Rd
index 4b6c3f0a..e50fb0e4 100644
--- a/man/plot_progeny_dosage_change.Rd
+++ b/man/plot_progeny_dosage_change.Rd
@@ -4,12 +4,14 @@
 \alias{plot_progeny_dosage_change}
 \title{Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error}
 \usage{
-plot_progeny_dosage_change(map_list, error)
+plot_progeny_dosage_change(map_list, error, verbose = T)
 }
 \arguments{
 \item{map_list}{a list of multiple \code{mappoly.map.list}}
 
 \item{error}{error rate used in global error in the `calc_genoprob_error()`}
+
+\item{verbose}{T or F for `calc_genoprob_error()` and `calc_homologprob()`}
 }
 \value{
 A ggplot of the changed and imputed genotypic dosages

From ceb4ddadf66b25c3c2fcd58ee888c6136e424b44 Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Fri, 16 Dec 2022 11:54:51 -0600
Subject: [PATCH 7/9] Update plot_progeny_dosage_change.R

---
 R/plot_progeny_dosage_change.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index a9ba2f32..1abf7bbc 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -144,4 +144,4 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   
 }
 
-str(empty_matrix)
+

From f01b849b8fc6577c497c823f88a7b6286b1737ae Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Tue, 29 Aug 2023 12:12:40 -0500
Subject: [PATCH 8/9] Update plot_progeny_dosage_change.R

Fixes:
1. fixed hard-coded ploidy
2. added the test map in for the automatic tests
3. made ploidy flexible for diploid up to octaploid
---
 R/plot_progeny_dosage_change.R | 82 ++++++++++++++++++++++++----------
 1 file changed, 58 insertions(+), 24 deletions(-)

diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index 1abf7bbc..38ebb9bd 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -1,7 +1,12 @@
 #' Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error
 #'
-#' Outputs a graphical representation ggplot with the percent of data changed
-#'
+#' Outputs a graphical representation ggplot with the percent of data changed. 
+#' 
+#' Most recent update 8/29/2023: 
+#'    -fixed issue where only worked on tetraploid to now working for diploid to octaploid.
+#'    -un-hardcoded linkage groups in maps. previously hard-coded for tetraploid rose.
+#'  
+#'  
 #' @param map_list a list of multiple \code{mappoly.map.list}
 #'
 #' @param error error rate used in global error in the `calc_genoprob_error()`
@@ -11,7 +16,8 @@
 #' @return A ggplot of the changed and imputed genotypic dosages
 #'
 #' @examples
-#'     plot_progeny_dosage_change(map_list=MAPs, error=0.05)
+#'     plot_progeny_dosage_change(map_list=solcap.dose.map, error=0.05)
+#'     
 #'
 #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
 #'
@@ -28,8 +34,8 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   
   print("calculating genoprob error")
   
-  genoprob  <- vector("list", 7)
-  for(i in 1:7){
+  genoprob  <- vector("list", length(map))
+  for(i in 1:length(map)){
     genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, verbose = verbose)
   }
   
@@ -84,7 +90,7 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   
   test <- sapply(homoprob_ind, function(x) {
     by_marker <- split.data.frame(x, x[,1]) 
-    final_matrix <- t(sapply(by_marker, function(y) y[order(y[,4], decreasing = T),][1:4,2]))
+    final_matrix <- t(sapply(by_marker, function(y) y[order(y[,4], decreasing = T),][1:ploidy,2]))
     final_vector <- apply(final_matrix, 1, function(w) paste0(w, collapse = ""))
     return(final_vector)
   })
@@ -95,22 +101,50 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   test=test[match(mrks,rownames(test)),]
   
   finished = test
-
   
+  if (ploidy==2){
+    for(a in 1:length(mrks)){
+      for(b in 1:length(inds)){
+        finished[a,b]=sum(PQ_matrix[a,substr(test[a,b], 1,1)],
+                          PQ_matrix[a,substr(test[a,b], 2,2)])}}
+  }  
+  
+  if (ploidy==4){
+    for(a in 1:length(mrks)){
+      for(b in 1:length(inds)){
+        finished[a,b]=sum(PQ_matrix[a,substr(test[a,b], 1,1)],
+                          PQ_matrix[a,substr(test[a,b], 2,2)],
+                          PQ_matrix[a,substr(test[a,b], 3,3)],
+                          PQ_matrix[a,substr(test[a,b], 4,4)])}}
+  }  
+  
+  if (ploidy==6){
+    for(a in 1:length(mrks)){
+      for(b in 1:length(inds)){
+        finished[a,b]=sum(PQ_matrix[a,substr(test[a,b], 1,1)],
+                          PQ_matrix[a,substr(test[a,b], 2,2)],
+                          PQ_matrix[a,substr(test[a,b], 3,3)],
+                          PQ_matrix[a,substr(test[a,b], 4,4)], 
+                          PQ_matrix[a,substr(test[a,b], 5,5)],
+                          PQ_matrix[a,substr(test[a,b], 6,6)])}}
+  }
   
-  for(a in 1:length(mrks)){
-    for(b in 1:length(inds)){
-      finished[a,b]=sum(PQ_matrix[a,substr(test[a,b], 1,1)],
-                        PQ_matrix[a,substr(test[a,b], 2,2)],
-                        PQ_matrix[a,substr(test[a,b], 3,3)],
-                        PQ_matrix[a,substr(test[a,b], 4,4)])
-      
-    }
-    #print(a)
+  if (ploidy==8){
+    for(a in 1:length(mrks)){
+      for(b in 1:length(inds)){
+        finished[a,b]=sum(PQ_matrix[a,substr(test[a,b], 1,1)],
+                          PQ_matrix[a,substr(test[a,b], 2,2)],
+                          PQ_matrix[a,substr(test[a,b], 3,3)],
+                          PQ_matrix[a,substr(test[a,b], 4,4)], 
+                          PQ_matrix[a,substr(test[a,b], 5,5)],
+                          PQ_matrix[a,substr(test[a,b], 6,6)],
+                          PQ_matrix[a,substr(test[a,b], 7,7)],
+                          PQ_matrix[a,substr(test[a,b], 8,8)])}}
   }
   
   
   
+  
   original_geno=as.matrix(dat$geno.dose[which(rownames(dat$geno.dose)%in%mrks),])
   original_geno=original_geno[,order(colnames(original_geno))]
   identical(colnames(finished), colnames(original_geno))
@@ -120,8 +154,8 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   original_geno[which(!original_geno==finished)]
   
   
-  percent_imputed=length(which(!original_geno==finished&original_geno==5))/length(original_geno)*100
-  percent_changed=length(which(!original_geno==finished&!original_geno==5))/length(original_geno)*100
+  percent_imputed=length(which(!original_geno==finished&original_geno==ploidy+1))/length(original_geno)*100
+  percent_changed=length(which(!original_geno==finished&!original_geno==ploidy+1))/length(original_geno)*100
   
   
   
@@ -129,15 +163,15 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
   colors = c("red","chartreuse","black")
   empty_matrix=matrix(0,nrow(original_geno),ncol(original_geno))
   empty_matrix[which(original_geno==finished)]="unchanged"
-  empty_matrix[which(!original_geno==finished&original_geno==5)]="imputed"
-  empty_matrix[which(!original_geno==finished&!original_geno==5)]="changed"
+  empty_matrix[which(!original_geno==finished&original_geno==ploidy+1)]="imputed"
+  empty_matrix[which(!original_geno==finished&!original_geno==ploidy+1)]="changed"
   empty_matrix_melt=melt(empty_matrix)
-  plot1<-ggplot(empty_matrix_melt, aes(Var1, Var2, fill= factor(value))) + 
-    geom_tile()+scale_fill_manual(values=colors)+
+  plot1<-ggplot(empty_matrix_melt, aes(Var1, Var2, fill= factor(value, levels=c("changed","imputed","unchanged")))) + 
+    geom_tile()+scale_fill_manual(values=colors, drop=F)+
     xlab("Markers")+
     ylab("Individuals")+
-    ggtitle(paste0("changed = ",round(percent_changed, digits=3),"% ","imputed = ", round(percent_imputed, digits=3),"%"))
-  
+    ggtitle(paste0("changed = ",round(percent_changed, digits=3),"% ","imputed = ", round(percent_imputed, digits=3),"%"))+
+    guides(fill=guide_legend(title="Dosage change"))
   print("done")
   
   return(plot1) 

From d706f24a7ebeecf7733ae3aebabbe028a31ae7a2 Mon Sep 17 00:00:00 2001
From: Jeekin Lau <jeekinlau@gmail.com>
Date: Tue, 29 Aug 2023 16:44:47 -0500
Subject: [PATCH 9/9] Update plot_progeny_dosage_change.Rd

---
 man/plot_progeny_dosage_change.Rd | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/man/plot_progeny_dosage_change.Rd b/man/plot_progeny_dosage_change.Rd
index e50fb0e4..a2f843b4 100644
--- a/man/plot_progeny_dosage_change.Rd
+++ b/man/plot_progeny_dosage_change.Rd
@@ -17,10 +17,16 @@ plot_progeny_dosage_change(map_list, error, verbose = T)
 A ggplot of the changed and imputed genotypic dosages
 }
 \description{
-Outputs a graphical representation ggplot with the percent of data changed
+Outputs a graphical representation ggplot with the percent of data changed.
+}
+\details{
+Most recent update 8/29/2023: 
+   -fixed issue where only worked on tetraploid to now working for diploid to octaploid.
+   -un-hardcoded linkage groups in maps. previously hard-coded for tetraploid rose.
 }
 \examples{
-    plot_progeny_dosage_change(map_list=MAPs, error=0.05)
+    plot_progeny_dosage_change(map_list=solcap.dose.map, error=0.05)
+    
 
 }
 \author{