Graphical analysis changes

robalexclark · Dec 9, 2021 · f19fc72 · f19fc72
1 parent 39fff86
commit f19fc72
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Showing 9 changed files with 128 additions and 197 deletions.
diff --git a/SilveR/Scripts/Common_Functions.R b/SilveR/Scripts/Common_Functions.R
@@ -700,26 +700,7 @@ NONCAT_SCAT <- function(typez) {
 	} else {
 		g10 <- g9
 	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow == "NULL" && YLimHigh == "NULL") {
-		g11 <- g10 + coord_cartesian(xlim=c(XLimLow, XLimHigh))
-	} else {
-		g11 <- g10
-	}
-
-	if (XLimLow == "NULL" && XLimHigh == "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g12 <- g11 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g12 <- g11
-	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g13 <- g12 + coord_cartesian(xlim=c(XLimLow, XLimHigh), ylim=c(YLimLow, YLimHigh))
-	} else {
-		g13 <- g12
-	}
-
-	suppressWarnings(print(g13))
+	suppressWarnings(print(g10))
 }
 
 
@@ -750,26 +731,7 @@ ONECATSEP_SCAT <- function() {
 	} else {
 		g3 <- g2
 	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow == "NULL" && YLimHigh == "NULL") {
-		g4 <- g3 + coord_cartesian(xlim=c(XLimLow, XLimHigh))
-	} else {
-		g4 <- g3
-	}
-
-	if (XLimLow == "NULL" && XLimHigh == "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g5 <- g4 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g5 <- g4
-	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(xlim=c(XLimLow, XLimHigh), ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-
-	suppressWarnings(print(g6))
+	suppressWarnings(print(g3))
 }
 
 TWOCATSEP_SCAT <- function() {
@@ -798,24 +760,7 @@ TWOCATSEP_SCAT <- function() {
 	} else {
 		g3 <- g2
 	}
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow == "NULL" && YLimHigh == "NULL") {
-		g4 <- g3 + coord_cartesian(xlim=c(XLimLow, XLimHigh))
-	} else {
-		g4 <- g3
-	}
-
-	if (XLimLow == "NULL" && XLimHigh == "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g5 <- g4 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g5 <- g4
-	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(xlim=c(XLimLow, XLimHigh), ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-	suppressWarnings(print(g6))
+	suppressWarnings(print(g3))
 }
 
 OVERLAID_SCAT <- function() {
@@ -852,25 +797,7 @@ OVERLAID_SCAT <- function() {
 	} else {
 		g4 <- g3
 	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow == "NULL" && YLimHigh == "NULL") {
-		g5 <- g4 + coord_cartesian(xlim=c(XLimLow, XLimHigh))
-	} else {
-		g5 <- g4
-	}
-
-	if (XLimLow == "NULL" && XLimHigh == "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-
-	if (XLimLow != "NULL" && XLimHigh != "NULL" && YLimLow != "NULL" && YLimHigh != "NULL") {
-		g7 <- g6 + coord_cartesian(xlim=c(XLimLow, XLimHigh), ylim=c(YLimLow, YLimHigh))
-	} else {
-		g7 <- g6
-	}
-	suppressWarnings(print(g7))
+	suppressWarnings(print(g4))
 }
 
 #===================================================================================================================
@@ -929,13 +856,7 @@ NONCAT_SEM <- function() {
 	} else {
 		g5 <- g4
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-	suppressWarnings(print(g6))
+	suppressWarnings(print(g5))
 }
 
 
@@ -995,13 +916,7 @@ ONECATSEP_SEM <- function() {
 	} else {
 		g5 <- g4
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-	suppressWarnings(print(g6))
+	suppressWarnings(print(g5))
 }
 
 
@@ -1061,13 +976,7 @@ TWOCATSEP_SEM <- function() {
 	} else {
 		g5 <- g4
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-	suppressWarnings(print(g6))
+	suppressWarnings(print(g5))
 }
 
 
@@ -1135,13 +1044,7 @@ OVERLAID_SEM <- function() {
 	} else {
 		g5 <- g4
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g6 <- g5 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g6 <- g5
-	}
-	suppressWarnings(print(g6))
+	suppressWarnings(print(g5))
 }
 
 #===================================================================================================================
@@ -1171,13 +1074,7 @@ NONCAT_CPP <- function() {
 	} else {
 		g2 <- g1
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g3 <- g2 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g3 <- g2
-	}
-	suppressWarnings(print(g3))
+	suppressWarnings(print(g2))
 }
 
 
@@ -1205,13 +1102,7 @@ ONECATSEP_CPP <- function() {
 	} else {
 		g2 <- g1
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g3 <- g2 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g3 <- g2
-	}
-	suppressWarnings(print(g3))
+	suppressWarnings(print(g2))
 }
 
 
@@ -1239,13 +1130,7 @@ TWOCATSEP_CPP <- function() {
 	} else {
 		g2 <- g1
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g3 <- g2 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g3 <- g2
-	}
-	suppressWarnings(print(g3))
+	suppressWarnings(print(g2))
 }
 
 
@@ -1266,13 +1151,7 @@ OVERLAID_CPP <- function() {
 	} else {
 		g1 <- g
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g2 <- g1 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g2 <- g1
-	}
-	suppressWarnings(print(g2))
+	suppressWarnings(print(g1))
 }
 
 #AUC case profiles plot - addition of extra area call
@@ -1323,13 +1202,7 @@ NONCAT_BOX <- function() {
 	} else {
 		g3 <- g2
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g4 <- g3 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g4 <- g3
-	}
-	suppressWarnings(print(g4))
+	suppressWarnings(print(g3))
 }
 
 
@@ -1367,13 +1240,7 @@ ONECATSEP_BOX <- function() {
 	} else {
 		g3 <- g2
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g4 <- g3 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g4 <- g3
-	}
-	suppressWarnings(print(g4))
+	suppressWarnings(print(g3))
 }
 
 
@@ -1412,13 +1279,7 @@ TWOCATSEP_BOX <- function() {
 	} else {
 		g3 <- g2
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g4 <- g3 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g4 <- g3
-	}
-	suppressWarnings(print(g4))
+	suppressWarnings(print(g3))
 }
 
 
@@ -1455,13 +1316,7 @@ OVERLAID_BOX <- function() {
 	} else {
 		g3 <- g2
 	}
-
-	if (YLimLow != "NULL" && YLimHigh != "NULL") {
-		g4 <- g3 + coord_cartesian(ylim=c(YLimLow, YLimHigh))
-	} else {
-		g4 <- g3
-	}
-	suppressWarnings(print(g4))
+	suppressWarnings(print(g3))
 }
 
 #===================================================================================================================

diff --git a/SilveR/Scripts/GraphicalAnalysis.R b/SilveR/Scripts/GraphicalAnalysis.R
@@ -41,17 +41,13 @@ ShowCaseIDsInLegend <- Args[29]
 ReferenceLine <- Args[30]
 DisplayLegend <-Args[31]
 displaypointSEM<-Args[32]
-XLimLow <- Args[33]
-XLimHigh<-Args[34]
-YLimLow<-Args[35]
-YLimHigh<- Args[36]
 
 #source(paste(getwd(),"/Common_Functions.R", sep=""))
 
 #Print args
-#if (Diplayargs == "Y"){
+if (Diplayargs == "Y"){
 	print(Args)
-#}
+}
 
 #===================================================================================================================
 #Setup the html file and associated css file

diff --git a/SilveR/Scripts/PairedTTestAnalysis.R b/SilveR/Scripts/PairedTTestAnalysis.R
@@ -1240,14 +1240,14 @@ if (showComps == "Y") {
 			if (inte==1) {
 				inte<-inte+1
 				if (dimfact ==2) {
-					add<-paste(add, ": The pairwise comparison is statistically significant at the ", sep="")
+					add<-paste(add, ": The pairwise comparison is statistically significant at the  ", sep="")
 				} else {
-					add<-paste(add, ": The following pairwise comparisons are statistically significant at the ", sep="")
+					add<-paste(add, ": The following pairwise comparisons are statistically significant at the  ", sep="")
 				}
 				add<-paste(add, 100*(1-sig), sep="")
-				add<-paste(add, "% level", sep="")
+				add<-paste(add, "% level ", sep="")
 				if (dimfact > 2) {
-					add<-paste(add, " : ", rows[i], sep="")
+					add<-paste(add, ": ", rows[i], sep="")
 				}
 			} else {
 				inte<-inte+1
@@ -1276,12 +1276,12 @@ if (showComps == "Y") {
 #Analysis description
 HTML.title("Analysis description", HR=2, align="left")
 
-add<-c("The data were analysed using ")
+add<-c("The data were analysed using an ")
 
 if (dimfact ==2 ) { #&& covariatelist == "NULL") {
-	add<-paste(add, "an extended paired t-test, with treatment factor ", timeFactor, sep="")
+	add<-paste(add, "extended paired t-test, with treatment factor ", timeFactor, sep="")
 } else {
-	add<-paste(add, "a repeated measures mixed model approach, with treatment factor ", timeFactor, sep="")
+	add<-paste(add, "repeated measures mixed model approach, with treatment factor ", timeFactor, sep="")
 }
 
 if (blocklist != "NULL" && covariatelist != "NULL")  {

diff --git a/SilveR/SilveR.csproj b/SilveR/SilveR.csproj
@@ -1,6 +1,6 @@
 <Project Sdk="Microsoft.NET.Sdk.Web">
   <PropertyGroup>
-    <Version>4.3.0</Version>
+    <Version>4.4.0</Version>
     <SignAssembly>true</SignAssembly>
     <AssemblyOriginatorKeyFile>SilveR.snk</AssemblyOriginatorKeyFile>
   </PropertyGroup>
@@ -15,8 +15,8 @@
 
   <PropertyGroup>
     <TargetFramework>net5.0</TargetFramework>
-    <AssemblyVersion>4.3.0.0</AssemblyVersion>
-    <FileVersion>4.3.0.0</FileVersion>
+    <AssemblyVersion>4.4.0.0</AssemblyVersion>
+    <FileVersion>4.4.0.0</FileVersion>
     <Nullable>disable</Nullable>
   </PropertyGroup>