R Under development (unstable) (2024-10-01 r87205 ucrt) -- "Unsuffered Consequences"
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> ### TEST-SUITE #####################################################################################
> # Description: This script runs the plotting code in BoutrosLab.plotting.general for testing purposes
> # The plots are stored in variables and plotted together in a single multiple in order to save plot-generation time
> 
> warning(paste(
+     'BPG will discontinue this test file in v8.0.0.',
+     'Instead, tests will use the standard testthat format.',
+     'For more information, see https://testthat.r-lib.org/'
+     ));
Warning message:
BPG will discontinue this test file in v8.0.0. Instead, tests will use the standard testthat format. For more information, see https://testthat.r-lib.org/ 
> 
> ### LOAD LIBRARY ###################################################################################
> library(BoutrosLab.plotting.general);
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: cluster
Loading required package: hexbin
Loading required package: grid

Attaching package: 'BoutrosLab.plotting.general'

The following object is masked from 'package:stats':

    dist

> 
> ### PLOTTING FUNCTIONS #############################################################################
> test.data <- data.frame(
+ 	x = 1:10,
+ 	y = LETTERS[1:10],
+ 	z = rnorm(10),
+ 	type = rep(LETTERS[1:2], 5),
+ 	stringsAsFactors = TRUE
+ 	);
> 
> # testing legend.grob
> covariate.legend <- list(
+ 	legend = list(
+ 		colours = default.colours(2),
+ 		labels = levels(test.data$type)[1:2]
+ 		)
+ 	);
> 
> legend.grob2 <- legend.grob(
+ 	legends = covariate.legend
+ 	);
Warning message:
In FUN(X[[i]], ...) : 'x' is NULL so the result will be NULL
> 
> # testing covariates.grob
> covariate.colours1 <- as.character(test.data$type);
> covariate.colours1[covariate.colours1 == 'A'] <- default.colours(2)[1];
> covariate.colours1[covariate.colours1 == 'B'] <- default.colours(2)[2];
> 
> # create an object to draw the covariates from
> covariates1 <- list(
+ 	rect = list(
+ 		col = 'black',
+ 		fill = covariate.colours1,
+ 		lwd = 1.5
+ 		)
+ 	);
> 
> covariates.grob1 <- covariates.grob(
+ 	covariates = covariates1,
+ 	ord = c(1:10),
+ 	side = 'top',
+ 	size = .8
+ 	);
> 
> barplot <- create.barplot(
+ 	formula = y ~ x,
+ 	data = test.data,
+ 	legend = list(
+ 		bottom = list(
+ 			fun = covariates.grob1
+ 			),
+ 		right = list(
+ 			fun = legend.grob2
+ 			),
+ 		inside = list(
+ 			fun = draw.key,
+ 			args = list(
+ 				key = get.corr.key(
+ 					x = test.data$x,
+ 					y = test.data$y,
+ 					label.items = c('spearman', 'spearman.p', 'kendall', 'beta1')
+ 					)
+ 				),
+ 			x = 0.5,
+ 			y = 0.5
+ 			)
+ 		),
+ 	description = 'testing metadata'
+ 	);
Warning messages:
1: In model.response(mf, "numeric") :
  using type = "numeric" with a factor response will be ignored
2: In Ops.factor(y, z$residuals) : '-' not meaningful for factors
> 
> # this isn't printed anywhere
> dend <- create.dendrogram(
+ 	x = data.frame(test.data$z, rnorm(10))
+ 	);
> 
> # # This is the slowest running function
> # heatmap <- create.heatmap(
> # 	x = as.matrix(test.data$z),
> # 	clustering.method = 'none'
> # 	);
> 
> dotmap <- create.dotmap(
+ 	x = test.data$z
+ 	);
> 
> hexbin <- create.hexbinplot(	
+ 	formula = z ~ x,
+ 	data = test.data
+ 	);
> 
> # Also using generate.at.final()
> density <- create.densityplot(
+ 	x = list(
+ 		a = test.data$x, 
+ 		b = test.data$z
+ 		),
+ 	xat = c(0, 1.1, 1.5, 1, 6, 4),
+ 	yat = c(0.34, 0.38, 0.7),
+ 	type = c('g', 'l'),
+ 	resolution = 100
+ 	);
> 
> manhattanplot <- create.manhattanplot(
+ 	formula = x ~ y,
+ 	data = test.data
+ 	);
> 
> polygonplot <- create.polygonplot(	
+ 	formula = NA ~ x,
+ 	data = test.data,
+ 	max = test.data$x,
+ 	min = test.data$z,
+ 	xlimits = c(0, 10),
+ 	ylimits = c(-2, 10)
+ 	);
> 
> qqcomp <- create.qqplot.comparison(
+ 	x = list(test.data$x, test.data$z)
+ 	);
> 
> scatter <- create.scatterplot(
+ 	formula = x ~ z,
+ 	data = test.data
+ 	);
> 
> seg <- create.segplot(
+ 	formula = y ~ x + z,
+ 	data = test.data
+ 	);
> 
> violin <- create.violinplot(
+ 	formula = y ~ z,
+ 	data = test.data
+ 	);
> 
> strip <- create.stripplot(
+ 	formula = z ~ y,
+ 	data = test.data
+ 	);
> 
> boxplot <- create.boxplot(
+ 	formula = x ~ y,
+ 	data = test.data
+ 	);
> 
> # these do not easily join the multiplot
> histogram <- create.histogram(
+ 	x = test.data$z
+ 	);
> 
> qqfit <- create.qqplot.fit(
+ 	x = test.data$z
+ 	);
> 
> # Plot everything in one plot for quicker running time
> create.multiplot(
+ 	file = NULL,
+ 	plot.objects = list(polygonplot, manhattanplot, hexbin, dotmap, density, qqcomp, scatter, seg, violin, barplot, strip, boxplot)
+ 	);
> 
> ### HELPER FUNCTIONS ###############################################################################
> 
> get.line.breaks(1:10);
[1] 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5 9.5
> 
> scientific.notation(1234, 2, type = 'list');
$base
[1] "1.23"

$exponent
[1] 3

> scientific.notation(0, 2);
[1] 0
> scientific.notation(c(1234, 1234), 1);
expression("1.2" %*% 10^3, "1.2" %*% 10^3)
> 
> # This returns the same thing as when type = 'expression' - should something be changed?
> scientific.notation(c(1234, 1234), 1, type = 'list');
expression("1.2" %*% 10^3, "1.2" %*% 10^3)
> 
> display.statistical.result(1234);
expression("P: 1200")
> 
> ### COLOUR FUNCTIONS ###############################################################################
> default.colours(12, is.greyscale = FALSE);
 [1] "orange"      "chartreuse4" "darkorchid4" "gold"        "dodgerblue" 
 [6] "firebrick3"  "yellowgreen" "darkorange1" "slateblue4"  "seagreen3"  
[11] "violetred3"  "turquoise3" 
> default.colours(5, palette.type = 'chromosomes', is.greyscale = FALSE);
[1] "darkred"     "firebrick1"  "pink1"       "darkorange3" "darkorange" 
> default.colours(5, palette.type = 'seq');
[1] "#C1D8AA" "#83B155" "#458B00" "#2E5C00" "#172E00"
> default.colours(c(4, 4), palette.type = c('seq', 'div'));
[[1]]
[1] "#C1D8AA" "#83B155" "#458B00" "#2E5C00"

[[2]]
[1] "#B32B2B" "#DD4E4E" "#EB7C7C" "#F7BEBE"

> 
> # display.colours(default.colours(3));
> # display.colours(grey(0.5));
> 
> force.colour.scheme(c('stopgain snv', 'splicing'), 'annovar.annotation');
[1] "orchid4" "gold1"  
> 
> proc.time()
   user  system elapsed 
   1.23    0.23    1.45