tests/testthat/test-other-null-data.R

In canvasXpress: Visualization Package for CanvasXpress in R

context("canvasXpress null data")
skip_if_offline(host = "www.canvasxpress.org")


get_plot_title <- function(plot) {
    paste(plot, "- Null Data should be dropped (not turn 0)")
}

set_NA_data <- function(y) {
    y[1, (2/5 * ncol(y)):(4/5 * ncol(y))] <- NA
    y
}

test_that("scatter2D null data", {
    tryCatch({
        y <- read.table("https://www.canvasxpress.org/data/cX-scatterR3-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-scatterR3-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')
    })

    y <- y[y$`logFC-X` > 1 & y$`logFC-Y` > 1, ]
    # Set some rows with X values NA, then rows with Y values NA, then both NA, followed by normal values
    y[1:(0.2*nrow(y)), 1]             <- NA
    y[(0.2*nrow(y)):(0.4*nrow(y)), 2] <- NA
    y[(0.4*nrow(y)):(0.6*nrow(y)), ]  <- NA
    z <- z[rownames(y), ]

    result <- canvasXpress(data            = y,
                           varAnnot        = z,
                           colorBy         = "Group",
                           graphType       = "Scatter2D",
                           title           = get_plot_title("Scatter2D"),
                           setMinX         = 0,
                           setMinY         = 0)

    check_ui_test(result)
})

test_that("Scatter3D null data", {
    tryCatch({
        y <- read.table("https://www.canvasxpress.org/data/cX-irist-dat.txt", header = TRUE, sep = "\t", quote = "", row.names = 1, fill = TRUE, check.names = FALSE, stringsAsFactors = FALSE)[, 1:3]
        z <- read.table("https://www.canvasxpress.org/data/cX-irist-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')
    })

    # Set some rows with X values NA, then rows with Y values NA, then both NA, followed by normal values
    y[1:(0.2*nrow(y)), 1]             <- NA
    y[(0.2*nrow(y)):(0.4*nrow(y)), 2] <- NA
    y[(0.4*nrow(y)):(0.6*nrow(y)), 3] <- NA
    y[(0.6*nrow(y)):(0.8*nrow(y)), ]  <- NA

    result <- canvasXpress(data            = y,
                           varAnnot        = z,
                           graphType       = "Scatter3D",
                           title           = get_plot_title("Scatter3D"),
                           xAxis           = list("Sepal.Length"),
                           yAxis           = list("Sepal.Width"),
                           zAxis           = list("Petal.Length"),
                           setMinX         = 0,
                           setMinY         = 0,
                           setMinZ         = 0)

    check_ui_test(result)
})

test_that("barplot null data", {
    tryCatch({
        y <- 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)
        x <- 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)
        y <- set_NA_data(y)
    },
    error = function(e) {
        skip('Unable to read data files')
    })

    result <-  canvasXpress(data                    = y,
                            smpAnnot                = x,
                            colorBy                 = "Drug Sensitivity",
                            graphOrientation        = "vertical",
                            graphType               = "Bar",
                            title                   = get_plot_title("Barplot"))

    check_ui_test(result)
})

test_that("boxplot null data", {
    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)
        y <- set_NA_data(y)
    },
    error = function(e) {
        skip('Unable to read data files')
    })

    x$Gene <- c(rep(c("Gene1", "Gene2"), 30))

    result <- canvasXpress(data                    = y,
                           smpAnnot                = x,
                           graphOrientation        = "vertical",
                           graphType               = "Boxplot",
                           colorBy                 = "supp",
                           groupingFactors         = list("supp", "dose"),
                           stringSampleFactors     = list("dose"),
                           segregateSamplesBy      = list("Gene"),
                           showBoxplotOriginalData = TRUE,
                           boxplotConnect          = TRUE,
                           showLegend              = TRUE,
                           smpLabelRotate          = 90,
                           smpTitle                = "Dose",
                           title                   = get_plot_title("Boxplot"),
                           xAxisTitle              = "len",
                           afterRender             = list(list("pivotX", list("supp"))))

    check_ui_test(result)
})

test_that("boxplot null smpdata", {
    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)
    },
    error = function(e) {
        skip('Unable to read data files')
    })

    # make some supp values NA
    x[c(1, 3, 5, 8, 10), "supp"] <- NA

    result <- canvasXpress(data                    = y,
                           smpAnnot                = x,
                           graphType               = "Boxplot",
                           smpTitle                = "Supp",
                           groupingFactors         = list("supp"),
                           colorBy                 = list("supp"),
                           title                   = "Sample Data with NA, should not cause the plot to crash")

    check_ui_test(result)
})