Fixed switching of alleles in nonrounded figures

Wedge-lab · Mar 4, 2017 · dee00a7 · dee00a7
1 parent 16eee6a
commit dee00a7
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/R/clonal_ascat.R b/R/clonal_ascat.R
@@ -1462,15 +1462,15 @@ runASCAT = function(lrr, baf, lrrsegmented, bafsegmented, chromosomes, dist_choi
 	  png(filename = copynumberprofilespng, width = 2000, height = 500, res = 200)
 	}
 	# clonal_runascat.plot2(rho_opt1, goodnessOfFit_opt1, ploidy_opt1, nA, nB, ch, lrr, bafsegmented, rConf, bConf, confidence)
-	ASCAT::ascat.plotAscatProfile(n1all = nB, n2all = nA, heteroprobes = TRUE, ploidy = ploidy_opt1, rho = rho_opt1, goodnessOfFit = goodnessOfFit_opt1, nonaberrant = FALSE, ch = ch, lrr = lrr, bafsegmented = bafsegmented)
+	ASCAT::ascat.plotAscatProfile(n1all = nA, n2all = nB, heteroprobes = TRUE, ploidy = ploidy_opt1, rho = rho_opt1, goodnessOfFit = goodnessOfFit_opt1, nonaberrant = FALSE, ch = ch, lrr = lrr, bafsegmented = bafsegmented)
 	if (!is.na(copynumberprofilespng)) { dev.off() }
 
 	# separated plotting from logic: create nonrounded copy number profile plot here
 	if (!is.na(nonroundedprofilepng)) {
 	  png(filename = nonroundedprofilepng, width = 2000, height = 500, res = 200)
 	}
 	# clonal_runascat.plot3(rho_opt1, goodnessOfFit_opt1, ploidy_opt1, nAfull, nBfull, ch, lrr, bafsegmented)
-	ASCAT::ascat.plotNonRounded(ploidy = ploidy_opt1, rho = rho_opt1, goodnessOfFit = goodnessOfFit_opt1, nonaberrant = FALSE, nAfull = nBfull, nBfull = nAfull, bafsegmented = bafsegmented, ch = ch, lrr = lrr)
+	ASCAT::ascat.plotNonRounded(ploidy = ploidy_opt1, rho = rho_opt1, goodnessOfFit = goodnessOfFit_opt1, nonaberrant = FALSE, nAfull = nAfull, nBfull = nBfull, bafsegmented = bafsegmented, ch = ch, lrr = lrr)
 	if (!is.na(nonroundedprofilepng)) { dev.off() }
 
   }
@@ -1629,15 +1629,15 @@ run_clonal_ASCAT = function(lrr, baf, lrrsegmented, bafsegmented, chromosomes, s
 	  png(filename = copynumberprofilespng, width = 2000, height = 500, res = 200)
 	}
 	# clonal_runascat.plot2(rho, goodnessOfFit, ploidy, nA, nB, ch, lrr, bafsegmented, rConf, bConf, confidence)
-	ASCAT::ascat.plotAscatProfile(n1all = nB, n2all = nA, heteroprobes = TRUE, ploidy = ploidy, rho = rho, goodnessOfFit = goodnessOfFit, nonaberrant = FALSE, ch = ch, lrr = lrr, bafsegmented = bafsegmented)
+	ASCAT::ascat.plotAscatProfile(n1all = nA, n2all = nB, heteroprobes = TRUE, ploidy = ploidy, rho = rho, goodnessOfFit = goodnessOfFit, nonaberrant = FALSE, ch = ch, lrr = lrr, bafsegmented = bafsegmented)
 	if (!is.na(copynumberprofilespng)) { dev.off() }
 
 	# separated plotting from logic: create nonrounded copy number profile plot here
 	if (!is.na(nonroundedprofilepng)) {
 	  png(filename = nonroundedprofilepng, width = 2000, height = 500, res = 200)
 	}
 	# clonal_runascat.plot3(rho, goodnessOfFit, ploidy, nAfull, nBfull, ch, lrr, bafsegmented)
-	ASCAT::ascat.plotNonRounded(ploidy = ploidy, rho = rho, goodnessOfFit = goodnessOfFit, nonaberrant = FALSE, nAfull = nBfull, nBfull = nAfull, bafsegmented = bafsegmented, ch = ch, lrr = lrr)
+	ASCAT::ascat.plotNonRounded(ploidy = ploidy, rho = rho, goodnessOfFit = goodnessOfFit, nonaberrant = FALSE, nAfull = nAfull, nBfull = nBfull, bafsegmented = bafsegmented, ch = ch, lrr = lrr)
 	if (!is.na(nonroundedprofilepng)) { dev.off() }
 
   }