Nothing
tests/testthat/test-other-decorations.R
In canvasXpress: Visualization Package for CanvasXpress in R
context("canvasXpress decorations")
test_that("scatterplot referenceLines", {
tryCatch({
data_y <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
data_z <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-var.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = data_y,
varAnnot = data_z,
colorBy = "Group",
colors = list("rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"),
graphType = "Scatter2D",
plotBox = FALSE,
showDecorations = TRUE,
sizeBy = "FC",
sizes = list(4, 14, 16, 18),
xAxis = list("logFC"),
yAxis = list("-log-pVal"),
showLegend = FALSE,
title = "Scatterplot - referenceLines",
decorations = list(line = list(list(color = "rgba(205,0,0,0.5)", width = 2, x = 0.5),
list(color = "rgba(0,104,139,0.5)", width = 2, x = -0.5))))
check_ui_test(result)
})
test_that("segregated scatterplot referenceLines", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-spider-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
z <- read.table("https://www.canvasxpress.org/data/cX-spider-var.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
varAnnot = z,
colorBy = "Response",
graphType = "Scatter2D",
segregateVariablesBy = list(list("Response")),
spiderBy = list(list("Subject")),
title = "Segregated Scatterplot - lines and labels",
xAxis = list("Weeks"),
yAxis = list("Change From Baseline %"),
decorations = list(line = list(list(color = "red", width = 2, x = 0, y = 0.8, x2 = 50, y2 = -0.8, scope = "Complete Response", label = "line1"),
list(color = "blue", width = 1, y = 0, scope = "Progressive Disease", label = "line2a"),
list(color = "blue", width = 1, x = 0, scope = "Progressive Disease", label = "line2b"),
list(color = "green", width = 3, x = 0, y = -0.8, x2 = 50, y2 = 0.8, scope = "Partial Response", label = "line3"))))
check_ui_test(result)
})
test_that("scatterplot notePoint", {
tryCatch({
data_y <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
data_z <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-var.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = data_y,
varAnnot = data_z,
colorBy = "Group",
colors = list("rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"),
graphType = "Scatter2D",
plotBox = FALSE,
showDecorations = TRUE,
sizeBy = "FC",
sizes = list(4, 14, 16, 18),
xAxis = list("logFC"),
yAxis = list("-log-pVal"),
showLegend = FALSE,
title = "Scatterplot - notePoint",
decorations = list(marker = list(list(sample = list("logFC", "-log-pVal"), text = "Maybe an Outlier?", variable = "Gene30", x = 0.11, y = 0.45))))
check_ui_test(result)
})
test_that("barplot annotations", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-basic2-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
graphType = "Bar",
graphOrientation = "vertical",
title = "Barplot - annotations",
decorations = list(marker = list(list(fontSize = 12, sample = "S1", text = "p < 0.01 ***", type = "annotation", variable = "V1", position = "top"),
list(fontSize = 12, sample = "S2", text = "p < 0.05 **", type = "annotation", variable = "V1", position = "top"))))
check_ui_test(result)
})
test_that("segregated barplot and boxplot marker decorations", {
tryCatch({
data <- iris %>%
mutate(Facet = paste0("facet_", seq(NROW(iris)) %% 2)) %>%
arrange(Facet, Species)
var_names <- c("Sepal.Length", "Sepal.Width")
markers_list <- list()
for (species in unique(data$Species)) {
for (facet in unique(data$Facet)) {
marker <- lapply(var_names, function(var_name) {
decoration_text <- paste0(var_name, ".", facet, ".", species) %>%
gsub("Sepal.", "", .) %>%
gsub("Length", "L", .) %>%
gsub("Width", "W", .) %>%
gsub("facet_", "", .)
list(text = decoration_text,
fontSize = 12,
type = "annotation",
variable = list(var_name),
sample = list(species),
scope = list(facet),
position = "top")
})
markers_list <- c(markers_list, marker)
}
}
},
error = function(e) {
skip('Unable to load data')
})
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Bar",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Barplot - marker decoration above each bar",
segregateSamplesBy = list(list("Facet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
decorations = list(marker = markers_list))
check_ui_test(result)
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Boxplot - marker decoration above each box",
segregateSamplesBy = list(list("Facet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
decorations = list(marker = markers_list))
check_ui_test(result)
})
test_that("double-segregated barplot and boxplot marker decorations", {
tryCatch({
data <- iris %>%
mutate(Facet = sample(c("facet_0", "facet_1", "NA"), size = NROW(iris), replace = TRUE),
OtherFacet = sample(c("facet_A", "NA"), size = NROW(iris), replace = TRUE)) %>%
arrange(Facet, OtherFacet, Species)
var_names <- c("Sepal.Length", "Sepal.Width")
markers_list <- list()
for (species in unique(data$Species)) {
for (facet in unique(data$Facet)) {
for (other_facet in unique(data$OtherFacet)) {
marker <- lapply(var_names, function(var_name) {
decoration_text <- paste0(var_name, ".", facet, ".", other_facet, ".", species) %>%
gsub("Sepal.", "", .) %>%
gsub("Length", "L", .) %>%
gsub("Width", "W", .) %>%
gsub("facet_", "", .)
list(text = decoration_text,
fontSize = 12,
type = "annotation",
variable = list(var_name),
sample = list(species),
scope = list(facet, other_facet),
position = "top")
})
markers_list <- c(markers_list, marker)
}
}
}
},
error = function(e) {
skip('Unable to load data')
})
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Bar",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Double-segregated Barplot - marker decoration above each bar",
segregateSamplesBy = list(list("Facet"), list("OtherFacet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
setMaxX = 1.1 * max(data[var_names]),
decorations = list(marker = markers_list))
check_ui_test(result)
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Double-segregated Boxplot - marker decoration above each box",
segregateSamplesBy = list(list("Facet"), list("OtherFacet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
setMaxX = 1.1 * max(data[var_names]),
decorations = list(marker = markers_list))
check_ui_test(result)
})
test_that("segregated Boxplot decorations with different values", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-iris-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
x <- read.table("https://www.canvasxpress.org/data/cX-iris-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
smpAnnot = x,
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Boxplot - decorations with different values for each Species",
segregateSamplesBy = list(list("Species")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
decorations = list(line = list(list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 2, width = 2, scope = "setosa"),
list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 4, width = 2, scope = "versicolor"),
list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 6, width = 2, scope = "virginica"))))
check_ui_test(result)
})
test_that("segregated Boxplot decorations with same values", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-iris-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)[, 1:100]
x <- read.table("https://www.canvasxpress.org/data/cX-iris-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)[1:100, , drop = FALSE]
y[, 1:50] <- y[, 1:50] - 2
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
smpAnnot = x,
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Boxplot - decoration should be on exactly the same height",
segregateSamplesBy = list(list("Species")),
groupingFactors = list("Species"),
layoutAdjust = FALSE,
decorations = list(line = list(list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 2, width = 2))))
check_ui_test(result)
})
test_that("segregated Boxplot decoration label position", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-toothgrowth-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
x <- read.table("https://www.canvasxpress.org/data/cX-toothgrowth-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
z <- data.frame(Gene = c("Gene1"), stringsAsFactors = FALSE)
rownames(z) <- rownames(y)
},
error = function(e) {
skip('Unable to read data files')
})
position_list <- list(left = "top", right = "bottom")
for (name in names(position_list)) {
pos <- position_list[[name]]
result <- canvasXpress(data = y,
smpAnnot = x,
varAnnot = z,
graphOrientation = "horizontal",
graphType = "Boxplot",
groupingFactors = list("dose"),
segregateVariablesBy = list(list("Gene")),
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "dose",
title = paste("Segregated Boxplot - decoration label position", pos),
layoutAdjust = TRUE,
decorations = list(line = list(list(align = name, color = "rgb(255,0,0)", label = "Decoration label", value = 20, width = 2, scope = "Gene1"))))
check_ui_test(result)
}
})
test_that("precalculated barplot - annotations", {
precalc.data <- data.frame(mean = c(5, 50, 250, 100, 150),
stdev = c(20, 10, 20, 15, 15),
stringsAsFactors = F)
precalc.data1 <- as.data.frame(t(precalc.data))
precalc.data2 <- as.data.frame(t(precalc.data))
colnames(precalc.data1) <- c("Group1", "Group2", "Group3", "Group4", "Group5")
colnames(precalc.data2) <- c("Group1", "Group2", "Group3", "Group1", "Group2")
smp.data <- matrix(data = c("Lev1", "Lev1", "Lev1", "Lev2", "Lev2"),
ncol = 1,
dimnames = list(colnames(precalc.data2), "level"))
# without smpAnnot data
result <- canvasXpress(data = precalc.data1,
graphType = "Bar",
graphOrientation = "vertical",
smpLabelFontStyle = "italic",
smpLabelRotate = 90,
showLegend = FALSE,
decorations = list(marker = list(list(fontSize = 10,
text = "Group3",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group3",
position = "top"),
list(fontSize = 10,
text = "Group4",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group4",
position = "top"))),
title = "Annotations for Precalculated Barplot without smpAnnot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
# with smpAnnot data
result <- canvasXpress(data = precalc.data2,
smpAnnot = smp.data,
segregateSamplesBy = list(list("level")),
graphType = "Bar",
graphOrientation = "vertical",
smpLabelFontStyle = "italic",
smpLabelRotate = 90,
showLegend = FALSE,
decorations = list(marker = list(list(fontSize = 10,
text = "Group3",
scope = "Lev1",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group3",
position = "top"),
list(fontSize = 10,
text = "Group1",
scope = "Lev2",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group1",
position = "top"))),
title = "Annotations for Precalculated Barplot with smpAnnot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
})
test_that("segregated and overlayed precalculated barplot - annotations", {
precalc.data <- data.frame(mean = c(100, 200, 150, 100, 50, 80, 250, 100, 150),
stdev = c(10, 20, 15, 15, 20, 10, 20, 15, 15),
stringsAsFactors = F)
precalc.data <- as.data.frame(t(precalc.data))
smp.data <- matrix(data = c("Lev1", "Lev1", "Lev1", "Lev1", "Lev2", "Lev2", "Lev2", "Lev2", "Lev2",
"Proj1", "Proj1", "Proj2", "Proj2", "Proj1", "Proj1", "Proj1", "Proj2", "Proj2"),
ncol = 2,
dimnames = list(colnames(precalc.data), c("level", "Project")))
result <- canvasXpress(data = precalc.data,
smpAnnot = smp.data,
segregateSamplesBy = list(list("level")),
smpOverlays = list("Project"),
graphType = "Bar",
graphOrientation = "vertical",
smpLabelFontStyle = "italic",
smpLabelRotate = 90,
showLegend = FALSE,
decorations = list(marker = list(list(fontSize = 10,
text = "(Lev1, V1)",
scope = list("Lev1"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V1"),
position = "top"),
list(fontSize = 10,
text = "(Lev2, V7)",
scope = list("Lev2"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V7"),
position = "top"),
list(fontSize = 10,
text = "(Lev2, V6)",
scope = list("Lev2"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V6"),
position = "top"),
list(fontSize = 10,
text = "(Lev1, V4)",
scope = list("Lev1"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V4"),
position = "top"))),
title = "Annotations for segregated and overlayed precalculated barplot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
})
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context("canvasXpress decorations")
test_that("scatterplot referenceLines", {
tryCatch({
data_y <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
data_z <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-var.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = data_y,
varAnnot = data_z,
colorBy = "Group",
colors = list("rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"),
graphType = "Scatter2D",
plotBox = FALSE,
showDecorations = TRUE,
sizeBy = "FC",
sizes = list(4, 14, 16, 18),
xAxis = list("logFC"),
yAxis = list("-log-pVal"),
showLegend = FALSE,
title = "Scatterplot - referenceLines",
decorations = list(line = list(list(color = "rgba(205,0,0,0.5)", width = 2, x = 0.5),
list(color = "rgba(0,104,139,0.5)", width = 2, x = -0.5))))
check_ui_test(result)
})
test_that("segregated scatterplot referenceLines", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-spider-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
z <- read.table("https://www.canvasxpress.org/data/cX-spider-var.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
varAnnot = z,
colorBy = "Response",
graphType = "Scatter2D",
segregateVariablesBy = list(list("Response")),
spiderBy = list(list("Subject")),
title = "Segregated Scatterplot - lines and labels",
xAxis = list("Weeks"),
yAxis = list("Change From Baseline %"),
decorations = list(line = list(list(color = "red", width = 2, x = 0, y = 0.8, x2 = 50, y2 = -0.8, scope = "Complete Response", label = "line1"),
list(color = "blue", width = 1, y = 0, scope = "Progressive Disease", label = "line2a"),
list(color = "blue", width = 1, x = 0, scope = "Progressive Disease", label = "line2b"),
list(color = "green", width = 3, x = 0, y = -0.8, x2 = 50, y2 = 0.8, scope = "Partial Response", label = "line3"))))
check_ui_test(result)
})
test_that("scatterplot notePoint", {
tryCatch({
data_y <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
data_z <- read.table("https://www.canvasxpress.org/data/cX-scatterR2-var.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = data_y,
varAnnot = data_z,
colorBy = "Group",
colors = list("rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"),
graphType = "Scatter2D",
plotBox = FALSE,
showDecorations = TRUE,
sizeBy = "FC",
sizes = list(4, 14, 16, 18),
xAxis = list("logFC"),
yAxis = list("-log-pVal"),
showLegend = FALSE,
title = "Scatterplot - notePoint",
decorations = list(marker = list(list(sample = list("logFC", "-log-pVal"), text = "Maybe an Outlier?", variable = "Gene30", x = 0.11, y = 0.45))))
check_ui_test(result)
})
test_that("barplot annotations", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-basic2-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
graphType = "Bar",
graphOrientation = "vertical",
title = "Barplot - annotations",
decorations = list(marker = list(list(fontSize = 12, sample = "S1", text = "p < 0.01 ***", type = "annotation", variable = "V1", position = "top"),
list(fontSize = 12, sample = "S2", text = "p < 0.05 **", type = "annotation", variable = "V1", position = "top"))))
check_ui_test(result)
})
test_that("segregated barplot and boxplot marker decorations", {
tryCatch({
data <- iris %>%
mutate(Facet = paste0("facet_", seq(NROW(iris)) %% 2)) %>%
arrange(Facet, Species)
var_names <- c("Sepal.Length", "Sepal.Width")
markers_list <- list()
for (species in unique(data$Species)) {
for (facet in unique(data$Facet)) {
marker <- lapply(var_names, function(var_name) {
decoration_text <- paste0(var_name, ".", facet, ".", species) %>%
gsub("Sepal.", "", .) %>%
gsub("Length", "L", .) %>%
gsub("Width", "W", .) %>%
gsub("facet_", "", .)
list(text = decoration_text,
fontSize = 12,
type = "annotation",
variable = list(var_name),
sample = list(species),
scope = list(facet),
position = "top")
})
markers_list <- c(markers_list, marker)
}
}
},
error = function(e) {
skip('Unable to load data')
})
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Bar",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Barplot - marker decoration above each bar",
segregateSamplesBy = list(list("Facet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
decorations = list(marker = markers_list))
check_ui_test(result)
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Boxplot - marker decoration above each box",
segregateSamplesBy = list(list("Facet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
decorations = list(marker = markers_list))
check_ui_test(result)
})
test_that("double-segregated barplot and boxplot marker decorations", {
tryCatch({
data <- iris %>%
mutate(Facet = sample(c("facet_0", "facet_1", "NA"), size = NROW(iris), replace = TRUE),
OtherFacet = sample(c("facet_A", "NA"), size = NROW(iris), replace = TRUE)) %>%
arrange(Facet, OtherFacet, Species)
var_names <- c("Sepal.Length", "Sepal.Width")
markers_list <- list()
for (species in unique(data$Species)) {
for (facet in unique(data$Facet)) {
for (other_facet in unique(data$OtherFacet)) {
marker <- lapply(var_names, function(var_name) {
decoration_text <- paste0(var_name, ".", facet, ".", other_facet, ".", species) %>%
gsub("Sepal.", "", .) %>%
gsub("Length", "L", .) %>%
gsub("Width", "W", .) %>%
gsub("facet_", "", .)
list(text = decoration_text,
fontSize = 12,
type = "annotation",
variable = list(var_name),
sample = list(species),
scope = list(facet, other_facet),
position = "top")
})
markers_list <- c(markers_list, marker)
}
}
}
},
error = function(e) {
skip('Unable to load data')
})
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Bar",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Double-segregated Barplot - marker decoration above each bar",
segregateSamplesBy = list(list("Facet"), list("OtherFacet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
setMaxX = 1.1 * max(data[var_names]),
decorations = list(marker = markers_list))
check_ui_test(result)
result <- canvasXpress(data = t(select(data, all_of(var_names))),
smpAnnot = t(data),
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Double-segregated Boxplot - marker decoration above each box",
segregateSamplesBy = list(list("Facet"), list("OtherFacet")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
setMaxX = 1.1 * max(data[var_names]),
decorations = list(marker = markers_list))
check_ui_test(result)
})
test_that("segregated Boxplot decorations with different values", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-iris-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
x <- read.table("https://www.canvasxpress.org/data/cX-iris-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
smpAnnot = x,
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Boxplot - decorations with different values for each Species",
segregateSamplesBy = list(list("Species")),
groupingFactors = list("Species"),
layoutAdjust = TRUE,
decorations = list(line = list(list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 2, width = 2, scope = "setosa"),
list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 4, width = 2, scope = "versicolor"),
list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 6, width = 2, scope = "virginica"))))
check_ui_test(result)
})
test_that("segregated Boxplot decorations with same values", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-iris-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)[, 1:100]
x <- read.table("https://www.canvasxpress.org/data/cX-iris-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)[1:100, , drop = FALSE]
y[, 1:50] <- y[, 1:50] - 2
},
error = function(e) {
skip('Unable to read data files')
})
result <- canvasXpress(data = y,
smpAnnot = x,
graphOrientation = "vertical",
graphType = "Boxplot",
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "Species",
title = "Segregated Boxplot - decoration should be on exactly the same height",
segregateSamplesBy = list(list("Species")),
groupingFactors = list("Species"),
layoutAdjust = FALSE,
decorations = list(line = list(list(align = "left", color = "rgb(255,0,0)", label = "Cutoff", value = 2, width = 2))))
check_ui_test(result)
})
test_that("segregated Boxplot decoration label position", {
tryCatch({
y <- read.table("https://www.canvasxpress.org/data/cX-toothgrowth-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
x <- read.table("https://www.canvasxpress.org/data/cX-toothgrowth-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
z <- data.frame(Gene = c("Gene1"), stringsAsFactors = FALSE)
rownames(z) <- rownames(y)
},
error = function(e) {
skip('Unable to read data files')
})
position_list <- list(left = "top", right = "bottom")
for (name in names(position_list)) {
pos <- position_list[[name]]
result <- canvasXpress(data = y,
smpAnnot = x,
varAnnot = z,
graphOrientation = "horizontal",
graphType = "Boxplot",
groupingFactors = list("dose"),
segregateVariablesBy = list(list("Gene")),
legendBox = FALSE,
smpLabelRotate = 90,
smpTitle = "dose",
title = paste("Segregated Boxplot - decoration label position", pos),
layoutAdjust = TRUE,
decorations = list(line = list(list(align = name, color = "rgb(255,0,0)", label = "Decoration label", value = 20, width = 2, scope = "Gene1"))))
check_ui_test(result)
}
})
test_that("precalculated barplot - annotations", {
precalc.data <- data.frame(mean = c(5, 50, 250, 100, 150),
stdev = c(20, 10, 20, 15, 15),
stringsAsFactors = F)
precalc.data1 <- as.data.frame(t(precalc.data))
precalc.data2 <- as.data.frame(t(precalc.data))
colnames(precalc.data1) <- c("Group1", "Group2", "Group3", "Group4", "Group5")
colnames(precalc.data2) <- c("Group1", "Group2", "Group3", "Group1", "Group2")
smp.data <- matrix(data = c("Lev1", "Lev1", "Lev1", "Lev2", "Lev2"),
ncol = 1,
dimnames = list(colnames(precalc.data2), "level"))
# without smpAnnot data
result <- canvasXpress(data = precalc.data1,
graphType = "Bar",
graphOrientation = "vertical",
smpLabelFontStyle = "italic",
smpLabelRotate = 90,
showLegend = FALSE,
decorations = list(marker = list(list(fontSize = 10,
text = "Group3",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group3",
position = "top"),
list(fontSize = 10,
text = "Group4",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group4",
position = "top"))),
title = "Annotations for Precalculated Barplot without smpAnnot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
# with smpAnnot data
result <- canvasXpress(data = precalc.data2,
smpAnnot = smp.data,
segregateSamplesBy = list(list("level")),
graphType = "Bar",
graphOrientation = "vertical",
smpLabelFontStyle = "italic",
smpLabelRotate = 90,
showLegend = FALSE,
decorations = list(marker = list(list(fontSize = 10,
text = "Group3",
scope = "Lev1",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group3",
position = "top"),
list(fontSize = 10,
text = "Group1",
scope = "Lev2",
type = "annotation",
variable = "precalculated BarChart",
sample = "Group1",
position = "top"))),
title = "Annotations for Precalculated Barplot with smpAnnot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
})
test_that("segregated and overlayed precalculated barplot - annotations", {
precalc.data <- data.frame(mean = c(100, 200, 150, 100, 50, 80, 250, 100, 150),
stdev = c(10, 20, 15, 15, 20, 10, 20, 15, 15),
stringsAsFactors = F)
precalc.data <- as.data.frame(t(precalc.data))
smp.data <- matrix(data = c("Lev1", "Lev1", "Lev1", "Lev1", "Lev2", "Lev2", "Lev2", "Lev2", "Lev2",
"Proj1", "Proj1", "Proj2", "Proj2", "Proj1", "Proj1", "Proj1", "Proj2", "Proj2"),
ncol = 2,
dimnames = list(colnames(precalc.data), c("level", "Project")))
result <- canvasXpress(data = precalc.data,
smpAnnot = smp.data,
segregateSamplesBy = list(list("level")),
smpOverlays = list("Project"),
graphType = "Bar",
graphOrientation = "vertical",
smpLabelFontStyle = "italic",
smpLabelRotate = 90,
showLegend = FALSE,
decorations = list(marker = list(list(fontSize = 10,
text = "(Lev1, V1)",
scope = list("Lev1"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V1"),
position = "top"),
list(fontSize = 10,
text = "(Lev2, V7)",
scope = list("Lev2"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V7"),
position = "top"),
list(fontSize = 10,
text = "(Lev2, V6)",
scope = list("Lev2"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V6"),
position = "top"),
list(fontSize = 10,
text = "(Lev1, V4)",
scope = list("Lev1"),
type = "annotation",
variable = list("precalculated BarChart"),
sample = list("V4"),
position = "top"))),
title = "Annotations for segregated and overlayed precalculated barplot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
})
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