context("canvasXpress duplicated labels")
test_that("segregated barplot duplicated labels", {
tryCatch({
data <- read.table("https://www.canvasxpress.org/data/cX-simple-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
smp_data <- read.table("https://www.canvasxpress.org/data/cX-simple-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
sample_names <- c("S1", "S2", "S4", "S4", "S5", "S1", "S4", "S4")
},
error = function(e) {
skip('Unable to read data files')
})
data <- cbind(data, data)
smp_data <- rbind(smp_data, smp_data)
smp_data$Gene <- c(rep("Gene1", length(sample_names)), rep("Gene2", length(sample_names)))
sample_names <- rep(sample_names, 2)
smp_data <- as.matrix(smp_data)
rownames(smp_data) <- colnames(data) <- sample_names
result <- canvasXpress(data = data,
smpAnnot = smp_data,
colorBy = "IC50",
graphOrientation = "vertical",
graphType = "Bar",
smpOverlays = list("Drug Sensitivity"),
segregateSamplesBy = list("Gene"),
smpTitle = "Cell Lines",
title = "Duplicated labels should appear correct for each Gene",
xAxis2Show = FALSE)
check_ui_test(result)
})
test_that("barplot duplicated labels", {
tryCatch({
data <- read.table("https://www.canvasxpress.org/data/cX-simple-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
smp_data <- read.table("https://www.canvasxpress.org/data/cX-simple-smp.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
sample_names <- c("S1", "S2", "S4", "S4", "S5", "S1", "S4", "S4")
},
error = function(e) {
skip('Unable to read data files')
})
smp_data <- as.matrix(smp_data)
rownames(smp_data) <- colnames(data) <- sample_names
result <- canvasXpress(data = data,
smpAnnot = smp_data,
colorBy = "IC50",
graphOrientation = "vertical",
graphType = "Bar",
smpOverlays = list("Drug Sensitivity"),
smpTitle = "Cell Lines",
title = "Duplicated labels should appear correct",
xAxis2Show = FALSE)
check_ui_test(result)
})
## Box plot tests
precalc.data <- data.frame(iqr1 = c(45, 7.3, 8, NA), qtl1 = c(109, 14.9, 4, NA),
median = c(159, 20.1, 7.25, NA), qtl3 = c(249, 26.2, 11.3, NA),
iqr3 = c(337, 40.6, 17.4, NA), outliers = c("", "44.5, 46", "", ""),
type = c("A", "B", "C", "D"),
stringsAsFactors = F)
sample_names <- c("Assault", "Rape", "Assault", "Missing")
test_that("segregated boxplot duplicated labels", {
precalc.data <- rbind(precalc.data, precalc.data)
precalc.data$cnty <- c(rep("Country1", length(sample_names)), rep("Country2", length(sample_names)))
sample_names <- rep(sample_names, 2)
precalc.data <- as.data.frame(t(precalc.data))
colnames(precalc.data) <- sample_names
result <- canvasXpress(data = precalc.data,
smpAnnot = precalc.data[c("type", "cnty"), ],
graphType = "Boxplot",
graphOrientation = "vertical",
smpTextFontStyle = "italic",
smpTextRotate = 90,
showLegend = FALSE,
segregateSamplesBy = list("cnty"),
title = "Precalculated boxplot with segregation - data with smpAnnot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
})
test_that("boxplot duplicated labels", {
precalc.data <- as.data.frame(t(precalc.data))
colnames(precalc.data) <- c("Assault", "Rape", "Assault", "Missing")
result <- canvasXpress(data = precalc.data,
smpAnnot = precalc.data["type", ],
graphType = "Boxplot",
graphOrientation = "vertical",
smpTextFontStyle = "italic",
smpTextRotate = 90,
showLegend = FALSE,
title = "Precalculated boxplot - data with smpAnnot",
titleScaleFontFactor = 0.5)
check_ui_test(result)
})
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