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Updating documentation and eliminating C++11 requirement
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,32 +1,34 @@ | ||
| #' Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error | ||
| #' Display genotypes imputed or changed by the HMM chain given a global genotypic error | ||
| #' | ||
| #' 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()` | ||
| #' @param verbose T or F for `calc_genoprob_error()` and `calc_homologprob()` | ||
| #' @param output_corrected TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output. | ||
| #' @param verbose if TRUE (default), current progress is shown; if FALSE, | ||
| #' no output is produced | ||
| #' @param output_corrected logical. if FALSE only the ggplot of the changed | ||
| #' dosage is printed, if TRUE then a new corrected dosage matrix is output. | ||
| #' | ||
| #' @return A ggplot of the changed and imputed genotypic dosages | ||
| #' | ||
| #' @examples | ||
| #' x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) # subset to run fast in tests | ||
| #' plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) # no new corrected dosages | ||
| #' corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected | ||
| #' x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) | ||
| #' plot_progeny_dosage_change(list(x), error=0.05, output_corrected=FALSE) | ||
| #' corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, | ||
| #' output_corrected=FALSE) #output corrected | ||
| #' | ||
| #' @author Jeekin Lau, \email{[email protected]}, with optimization by Cristiane Taniguti, \email{[email protected]} | ||
| #' @author Jeekin Lau, \email{[email protected]}, with optimization by Cristiane | ||
| #' Taniguti, \email{[email protected]} | ||
| #' | ||
| #' @import ggplot2 | ||
| #' @import reshape2 | ||
| #' @export plot_progeny_dosage_change | ||
|
|
||
| plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_corrected=F){ | ||
| plot_progeny_dosage_change <- function(map_list, | ||
| error, | ||
| verbose = TRUE, | ||
| output_corrected = FALSE){ | ||
| Var1 <- Var2 <- value <- NULL | ||
| map=map_list | ||
| if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here") | ||
|
|
@@ -38,7 +40,8 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc | |
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| genoprob <- vector("list", length(map)) | ||
| for(i in 1:length(map)){ | ||
| genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, verbose = verbose) | ||
| genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, | ||
| verbose = verbose) | ||
| } | ||
|
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||
| print("calculating homologprob") | ||
|
|
@@ -47,8 +50,8 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc | |
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| print("comparing to orginal") | ||
|
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| 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=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$P), recursive=FALSE) | ||
| Q=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$Q), recursive=FALSE) | ||
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@@ -92,7 +95,7 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc | |
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| 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:ploidy,2])) | ||
| final_matrix <- t(sapply(by_marker, function(y) y[order(y[,4], decreasing = TRUE),][1:ploidy,2])) | ||
| final_vector <- apply(final_matrix, 1, function(w) paste0(w, collapse = "")) | ||
| return(final_vector) | ||
| }) | ||
|
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@@ -169,15 +172,15 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc | |
| 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, levels=c("changed","imputed","unchanged")))) + | ||
| geom_tile()+scale_fill_manual(values=colors, drop=F)+ | ||
| geom_tile()+scale_fill_manual(values=colors, drop=FALSE)+ | ||
| xlab("Markers")+ | ||
| ylab("Individuals")+ | ||
| ggtitle(paste0("changed = ",round(percent_changed, digits=3),"% ","imputed = ", round(percent_imputed, digits=3),"%"))+ | ||
| guides(fill=guide_legend(title="Dosage change")) | ||
| print("done") | ||
|
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| print(plot1) | ||
| if (output_corrected ==T){ | ||
| if (output_corrected ==TRUE){ | ||
| mrk_names=rownames(finished) | ||
| mrk_index=which(dat$mrk.names%in%mrk_names) | ||
| P1 = dat$dosage.p1[mrk_index] | ||
|
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