R Under development (unstable) (2024-09-03 r87093 ucrt) -- "Unsuffered Consequences"
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> library(RCytoGPS)
> ## simulate data
> set.seed(53106)
> CL <- RCytoGPS:::cytobandLocations
> fake <- as.data.frame(matrix(runif(nrow(CL) * 10), ncol = 10))
> fake$PV <- runif(nrow(fake), 0, 1)
> CL <- cbind(CL, fake) # extra colnames V1, ..., V10
> CD <- CytobandData(CL)
> 
> try( image(CD))     # fails, since you need 'chr'
Error in .local(x, ...) : argument "chr" is missing, with no default
> try( image(CD, 3) ) # fails, since you also need 'what'
Error in .local(x, ...) : argument "what" is missing, with no default
> 
> ### windows(width=16, height=16)
> ## (plot1Chrom) one chromsome, stacks, vertical
> image(CD, chr = 1, what = "V1", debug = TRUE)
plot1Chrom
> image(CD, chr = 1, what = c("V1", "V2"), debug = TRUE)
plot1Chrom
> image(CD, chr = 13, what = c("V1", "V2", "V3","V4", "V5", "V6"), debug = TRUE)
plot1Chrom
> image(CD, chr = 6, what = paste("V", 1:10, sep=""), debug = TRUE)
plot1Chrom
> 
> ## (plot1Chrom) one chromosome, stacks, horizontal
> image(CD, 6, paste("V", 1:2, sep=""), horiz = TRUE, debug = TRUE)
plot1Chrom
> image(CD, 6, paste("V", 1:2, sep=""), axes = FALSE, debug = TRUE)
plot1Chrom
> image(CD, 6, paste("V", 1:2, sep=""), horiz = TRUE, axes = FALSE, debug = TRUE)
plot1Chrom
> 
> image(CD, 8, paste("V", 1:2, sep=""), horiz = FALSE,
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(127, 192))
> 
> image(CD, 8, paste("V", 1:2, sep=""), horiz = TRUE,
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(127, 192), debug = TRUE)
plot1Chrom
> 
> # combined (plot1Chrom)
> opar <- par(mfrow=c(2,1))
> image(CD, 2, c("V1", "V2", "V3"), debug = TRUE)
plot1Chrom
> image(CD, 13, c("V4", "V5", "V6"), debug = TRUE)
plot1Chrom
> par(opar)
> 
> ## (makeIdiogram)
> image(CD, "all", "V10", pal = "forestgreen", debug = TRUE) # no names  is better
makeIdiogram
> image(CD, "all", "V10", pal = "forestgreen", debug = TRUE, axes = TRUE) # names
makeIdiogram
> image(CD, "all", "V10", pal = "forestgreen", legend = TRUE, debug = TRUE)
makeIdiogram
> image(CD, "all", "V10", pal = "forestgreen", debug = TRUE,
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(63, 155))
makeIdiogram
> 
> ## (plot2Chrom) one chromosome, two-sided
> image(CD, 3, list("V1", "V2"), debug = TRUE) # default axes = TRUE and horiz = FALSE
plot2Chrom
> image(CD, 3, list("V1", "V2"), axes = FALSE, debug = FALSE)
> image(CD, 3, list("V1", "V2"), horiz = TRUE, debug = TRUE)
plot2Chrom
> image(CD, 3, list("V1", "V2"), horiz = TRUE, axes = FALSE, debug = TRUE) # still names?
plot2Chrom
> 
> image(CD, 8, list("V1", "V2"),
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(127, 192),
+       debug = TRUE)
plot2Chrom
> image(CD, 8, list("V1", "V2"), horiz = TRUE,
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(127, 192),
+       debug = TRUE)
plot2Chrom
> 
> ## (biIdiogram)
> image(CD, chr = "all", list("V1", "V2"), horiz=TRUE, debug = TRUE) # default axes = FALSE
biIdiogram
> image(CD, chr = "all", list("V1", "V2"), horiz=FALSE, debug  = TRUE)
biIdiogram
> image(CD, chr = "all", list("V1", "V2"), horiz=TRUE, axes = TRUE, debug = TRUE)
biIdiogram
> image(CD, chr = "all", list("V1", "V2"), horiz=FALSE, axes = TRUE, debug  = TRUE)
biIdiogram
> image(CD, chr = "all", list("V1", "V2"), horiz=TRUE, nrows = 3)
> image(CD, chr = "all", list("V1", "V2"), horiz=FALSE, nrows = 3)
> image(CD, chr = "all", list("V1", "V2"), horiz=TRUE, nrows = 4)
> image(CD, chr = "all", list("V1", "V2"), horiz=FALSE, nrows = 4)
> image(CD, chr = "all", list("V1", "V2"), horiz=TRUE, nrows = 1)
> image(CD, chr = "all", list("V1", "V2"), horiz=FALSE, nrows = 1)
> ## still need to test legend and sigcolumn
> image(CD, chr = "all", list("V1", "V2"), horiz=TRUE, legend = TRUE, debug = TRUE)
biIdiogram
> image(CD, chr = "all", list("V1", "V2"), horiz=FALSE, legend = TRUE, debug  = TRUE)
biIdiogram
> 
> image(CD, chr = "all", list("V1", "V2"),
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(127, 192),
+       debug = TRUE)
biIdiogram
> image(CD, chr = "all", list("V1", "V2"), horiz = TRUE,
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(127, 192),
+       debug = TRUE)
biIdiogram
> 
> # stackIdiograms
> mycolumns <- paste("V", 1:3, sep="")
> image(CD, chr = "all", mycolumns, debug = TRUE)
stackIdiogram
> image(CD, chr = "all", mycolumns, nrows = 3, debug = TRUE)
stackIdiogram
> image(CD, chr = "all", mycolumns, nrows = 4, horiz=FALSE, debug = TRUE)
stackIdiogram
> image(CD, chr = "all", mycolumns, nrows = 4, horiz=TRUE, debug = TRUE)
stackIdiogram
> image(CD, chr = "all", mycolumns, nrows = 4, axes=TRUE, horiz=FALSE, debug = TRUE)
stackIdiogram
> image(CD, chr = "all", mycolumns, nrows = 4, axes=TRUE, horiz=TRUE, debug = TRUE)
stackIdiogram
> ## still need to check axes, legend, and sigcolumn
> 
> image(CD, chr = "all", mycolumns, debug = TRUE, legend = TRUE) # no good place to put it
stackIdiogram
> image(CD, chr = "all", mycolumns, horiz = TRUE, debug = TRUE, legend = TRUE) # no good place to put it
stackIdiogram
> 
> 
> image(CD, chr = "all", mycolumns, horiz = TRUE,
+       sigcolumn = "PV", sigcut = c(0.01, 0.05), alpha = c(63, 155),
+       debug = TRUE)
stackIdiogram
> 
> proc.time()
   user  system elapsed 
  30.42    5.01   35.54