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Merge pull request #68 from jeekinlau/main
update plot_progeny_dosage_change
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -11,21 +11,22 @@ | |
| #' | ||
| #' @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. | ||
| #' | ||
| #' @return A ggplot of the changed and imputed genotypic dosages | ||
| #' | ||
| #' @examples | ||
| #' x<-get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) | ||
| #' plot_progeny_dosage_change(list(x), error=0.05) | ||
| #' 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 | ||
| #' | ||
| #' @author Jeekin Lau, \email{[email protected]}, with optimization by Cristiane Taniguti, \email{[email protected]} | ||
| #' | ||
| #' @import ggplot2 | ||
| #' @import reshape2 | ||
| #' @export plot_progeny_dosage_change | ||
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| plot_progeny_dosage_change <- function(map_list, error, verbose=T){ | ||
| plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_corrected=F){ | ||
| Var1 <- Var2 <- value <- NULL | ||
| map=map_list | ||
| if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here") | ||
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@@ -175,8 +176,17 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){ | |
| guides(fill=guide_legend(title="Dosage change")) | ||
| print("done") | ||
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| return(plot1) | ||
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| print(plot1) | ||
| if (output_corrected ==T){ | ||
| mrk_names=rownames(finished) | ||
| mrk_index=which(dat$mrk.names%in%mrk_names) | ||
| P1 = dat$dosage.p1[mrk_index] | ||
| P2 = dat$dosage.p2[mrk_index] | ||
| sequence = dat$chrom[mrk_index] | ||
| sequence_position = dat$genome.pos[mrk_index] | ||
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| hmm_imputed = cbind(P1,P2,sequence,sequence_position, finished) | ||
| return(hmm_imputed)} | ||
| } | ||
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