Revert test function removal

tests/test_plotting_functions.R

@@ -0,0 +1,194 @@
+### 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/'
+    ));
+
+### LOAD LIBRARY ###################################################################################
+library(BoutrosLab.plotting.general);
+
+### 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$type)[1:2]
+		)
+	);
+
+legend.grob2 <- legend.grob(
+	legends = covariate.legend
+	);
+
+# testing covariates.grob
+covariate.colours1 <- as.character(test.data$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'
+	);
+
+# 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);
+
+scientific.notation(1234, 2, type = 'list');
+scientific.notation(0, 2);
+scientific.notation(c(1234, 1234), 1);
+
+# This returns the same thing as when type = 'expression' - should something be changed?
+scientific.notation(c(1234, 1234), 1, type = 'list');
+
+display.statistical.result(1234);
+
+### COLOUR FUNCTIONS ###############################################################################
+default.colours(12, is.greyscale = FALSE);
+default.colours(5, palette.type = 'chromosomes', is.greyscale = FALSE);
+default.colours(5, palette.type = 'seq');
+default.colours(c(4, 4), palette.type = c('seq', 'div'));
+
+# display.colours(default.colours(3));
+# display.colours(grey(0.5));
+
+force.colour.scheme(c('stopgain snv', 'splicing'), 'annovar.annotation');