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Add SVG output support with transparent background #152

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Merged
hyacz merged 1 commit into from
May 8, 2026
+9 −1
Merged

Add SVG output support with transparent background #152

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10 changes: 9 additions & 1 deletion R/CMplot.r
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ CMplot <- function(
conf.int.col=NULL,
file.output=TRUE,
file.name=NULL,
file=c("jpg","pdf","tiff","png"),
file=c("jpg","pdf","tiff","png","svg"),
dpi=300,
height=NULL,
width=NULL,
Expand Down Expand Up @@ -634,6 +634,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Marker_Density.",ifelse(is.null(file.name),taxa,file.name[1]),".pdf",sep=""), width=wh,height=ht)
if(file=="tiff") tiff(paste("Marker_Density.",ifelse(is.null(file.name),taxa,file.name[1]),".tiff",sep=""), width=wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("Marker_Density.",ifelse(is.null(file.name),taxa,file.name[1]),".png",sep=""), width=wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("Marker_Density.",ifelse(is.null(file.name),taxa,file.name[1]),".svg",sep=""), width=wh,height=ht,bg="transparent")
# par(xpd=TRUE)
par(mar=c(mar[1]-2, mar[2]-1, mar[3]+1, mar[4]))
}else{
Expand Down Expand Up @@ -878,6 +879,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Cir_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".pdf",sep=""), width=wh,height=ht)
if(file=="tiff") tiff(paste("Cir_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".tiff",sep=""), width=wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("Cir_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".png",sep=""), width=wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("Cir_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".svg",sep=""), width=wh,height=ht,bg="transparent")
par(pty="s", xpd=TRUE, mar=c(1,1,1,1))
}
if(!file.output){
Expand Down Expand Up @@ -1450,6 +1452,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Multi-tracks_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".pdf",sep=""), width=wh,height=ht*R)
if(file=="tiff") tiff(paste("Multi-tracks_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".tiff",sep=""), width=wh*dpi,height=ht*dpi*R,res=dpi)
if(file=="png") png(paste("Multi-tracks_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".png",sep=""), width=wh*dpi,height=ht*dpi*R,res=dpi,bg=NA)
if(file=="svg") svg(paste("Multi-tracks_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".svg",sep=""), width=wh,height=ht*R,bg="transparent")
par(mfcol=c(R,1), xaxs="i")
}
if(!file.output){
Expand Down Expand Up @@ -1643,6 +1646,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Multi-traits_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".pdf",sep=""), width=wh,height=ht)
if(file=="tiff") tiff(paste("Multi-traits_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".tiff",sep=""), width=wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("Multi-traits_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".png",sep=""), width=wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("Multi-traits_Manhtn.",ifelse(is.null(file.name),taxa,file.name[1]),".svg",sep=""), width=wh,height=ht,bg="transparent")
if(!is.null(legend.ncol) && legend.pos=="middle"){
mar[3] = mar[3] + ceiling(length(trait) / legend.ncol)
}
Expand Down Expand Up @@ -1936,6 +1940,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Rect_Manhtn.",ifelse(is.null(file.name),trait[i],file.name[i]),".pdf",sep=""), width=wh,height=ht)
if(file=="tiff") tiff(paste("Rect_Manhtn.",ifelse(is.null(file.name),trait[i],file.name[i]),".tiff",sep=""), width=wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("Rect_Manhtn.",ifelse(is.null(file.name),trait[i],file.name[i]),".png",sep=""), width=wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("Rect_Manhtn.",ifelse(is.null(file.name),trait[i],file.name[i]),".svg",sep=""), width=wh,height=ht,bg="transparent")
par(mar=mar,xaxs="i",yaxs="r")
}
if(!file.output){
Expand Down Expand Up @@ -2193,6 +2198,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Multi-tracks_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".pdf",sep=""), width=R*wh,height=ht)
if(file=="tiff") tiff(paste("Multi-tracks_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".tiff",sep=""), width=R*wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("Multi-tracks_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".png",sep=""), width=R*wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("Multi-tracks_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".svg",sep=""), width=R*wh,height=ht,bg="transparent")
par(mfcol=c(1,R),xpd=TRUE)
}else{
ht=ifelse(is.null(height), 5.5, height)
Expand Down Expand Up @@ -2311,6 +2317,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("Multi-traits_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".pdf",sep=""), width=wh,height=ht)
if(file=="tiff") tiff(paste("Multi-traits_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".tiff",sep=""), width=wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("Multi-traits_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".png",sep=""), width=wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("Multi-traits_QQplot.",ifelse(is.null(file.name),taxa,file.name[1]),".svg",sep=""), width=wh,height=ht,bg="transparent")
par(mar=c(mar[2],mar[2],mar[3],mar[4]),xpd=TRUE)
}else{
ht=ifelse(is.null(height), 5.5, height)
Expand Down Expand Up @@ -2439,6 +2446,7 @@ CMplot <- function(
if(file=="pdf") pdf(paste("QQplot.",ifelse(is.null(file.name),trait[i],file.name[i]),".pdf",sep=""), width=wh,height=ht)
if(file=="tiff") tiff(paste("QQplot.",ifelse(is.null(file.name),trait[i],file.name[i]),".tiff",sep=""), width=wh*dpi,height=ht*dpi,res=dpi)
if(file=="png") png(paste("QQplot.",ifelse(is.null(file.name),trait[i],file.name[i]),".png",sep=""), width=wh*dpi,height=ht*dpi,res=dpi,bg=NA)
if(file=="svg") svg(paste("QQplot.",ifelse(is.null(file.name),trait[i],file.name[i]),".svg",sep=""), width=wh,height=ht,bg="transparent")
par(mar=c(mar[2],mar[2],mar[3],mar[4]),xpd=TRUE)
}else{
ht=ifelse(is.null(height), 5.5, height)
Expand Down