tests/testthat/test-getData.R
In fionarhuang/treeclimbR: An algorithm to find optimal signal levels in a tree
test_that("getData works", {
## Generate some data
## -------------------------------------------------------------------------
library(TreeSummarizedExperiment)
library(ggtree)
library(ggplot2)
library(ggnewscale)
library(viridis)
library(dplyr)
data(tinyTree)
## Simulate data with 10 features and 10 samples (5 from each of 2 groups)
p1 <- c(rep(0.1/3, 3), rep(0.4/2, 2), rep(0.1, 5))
p2 <- c(rep(0.4/3, 3), rep(0.1/2, 2), rep(0.1, 5))
set.seed(1)
ct0 <- cbind(rmultinom(n = 5, size = 50, prob = p1),
rmultinom(n = 5, size = 50, prob = p2))
colnames(ct0) <- paste("S", seq_len(10), sep = "")
rownames(ct0) <- convertNode(tree = tinyTree, node = seq_len(10))
oo <- sample(seq_len(10))
ct0 <- ct0[, oo]
ct <- rbind(colSums(ct0[seq(1, 3), ]), colSums(ct0[seq(4, 5), ]),
ct0[seq(6, 10), ])
colnames(ct) <- paste("S", seq_len(10), sep = "")
rownames(ct) <- convertNode(tree = tinyTree, node = c(13, 18, seq(6, 10)))
col_split <- ifelse(colnames(ct) %in% paste0("S", seq_len(5)), "A", "B")
names(col_split) <- colnames(ct)
## Prepare the heatmaps
tree_fig <- ggtree(tinyTree, branch.length = "none",
layout = "rectangular", open.angle = 100) +
geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
geom_hilight(node = 13, fill = "blue", alpha = 0.3)
fig <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue"
)
## Figure with row names
figrn <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE
)
## Figure with scaled tree
tree_fig_sc <- ggtree(tinyTree, branch.length = "none",
layout = "rectangular", open.angle = 100)
tree_fig_sc <- ggtree::scaleClade(tree_fig_sc, node = 15, scale = 4)
tree_fig_sc <- ggtree::scaleClade(tree_fig_sc, node = 14, scale = 0.25) +
geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
geom_hilight(node = 13, fill = "blue", alpha = 0.3)
figsc <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig_sc, hm_data = ct,
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE, rownames_hjust = 0, rownames_offset_x = 0.1
)
## Provide column order -> ignore cluster_column
expect_warning({
figco <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
column_order = paste0("S", seq_len(10)),
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE
)}, "column_order is ignored when column_split is given")
expect_warning({
figco <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
column_order = paste0("S", seq_len(10)),
cluster_column = TRUE, column_split = NULL,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE
)}, "cluster_column is ignored because column_order is given")
## Check that the function fails with wrong input
## -------------------------------------------------------------------------
expect_error(getData(tree_hm = 1, type = "heatmap"),
"'tree_hm' must be of class 'ggtree'")
expect_error(getData(tree_hm = fig, type = "missing"),
"'arg' should be one of")
## Check that the function works with correct input
## -------------------------------------------------------------------------
## Heatmap data
df_hm <- getData(tree_hm = fig, type = "heatmap")
expect_s3_class(df_hm, "data.frame")
expect_equal(nrow(df_hm), 70) ## 7 blocks, 10 samples
expect_named(df_hm, c("node", "row_label", "x", "y", "height", "width",
"variable", "value", "column_order", "split_level"))
expect_equal(df_hm$row_label, rep(rownames(ct), each = 10))
expect_equal(df_hm$column_order, rep(c(2, 3, 4, 0, 1, 5, 6, 8, 9, 7), 7))
expect_equal(df_hm$variable, factor(rep(paste0("S", seq_len(10)), 7),
levels = c("S4", "S5", "S1", "S2", "S3",
"S6", "S7", "S10", "S8",
"S9")))
expect_true(all(diff(df_hm$x[order(df_hm$column_order)]) >= 0))
expect_length(unique(paste(df_hm$column_order, df_hm$x)), 10)
expect_equal(unique(df_hm$width), 0.6)
expect_equal(unique(df_hm$split_level[df_hm$variable == "S1"]), 0)
expect_equal(unique(df_hm$split_level[df_hm$variable == "S8"]), 1)
expect_equal(unique(df_hm$height[df_hm$row_label == "Node_13"]), 3)
expect_equal(unique(df_hm$height[df_hm$row_label == "Node_18"]), 2)
expect_equal(unique(df_hm$height[df_hm$row_label == "t8"]), 1)
for (n in rownames(ct)) {
for (m in colnames(ct)) {
expect_equal(df_hm$value[df_hm$variable == m &
df_hm$row_label == n],
ct[n, m])
}
}
## ... from figure with row names
df_hm_rn <- getData(tree_hm = figrn, type = "heatmap")
expect_equal(df_hm, df_hm_rn)
## ... from figure with scaled tree
df_hm_sc <- getData(tree_hm = figsc, type = "heatmap")
expect_s3_class(df_hm_sc, "data.frame")
expect_equal(nrow(df_hm_sc), 70) ## 7 blocks, 10 samples
expect_named(df_hm_sc, c("node", "row_label", "x", "y", "height", "width",
"variable", "value", "column_order", "split_level"))
expect_equal(df_hm_sc$row_label, rep(rownames(ct), each = 10))
expect_equal(df_hm_sc$column_order, rep(c(2, 3, 4, 0, 1, 5, 6, 8, 9, 7), 7))
expect_equal(df_hm_sc$variable, factor(rep(paste0("S", seq_len(10)), 7),
levels = c("S4", "S5", "S1", "S2", "S3",
"S6", "S7", "S10", "S8",
"S9")))
expect_true(all(diff(df_hm_sc$x[order(df_hm_sc$column_order)]) >= 0))
expect_length(unique(paste(df_hm_sc$column_order, df_hm_sc$x)), 10)
expect_equal(unique(df_hm_sc$width), 0.6)
expect_equal(unique(df_hm_sc$split_level[df_hm_sc$variable == "S1"]), 0)
expect_equal(unique(df_hm_sc$split_level[df_hm_sc$variable == "S8"]), 1)
expect_equal(unique(df_hm_sc$height[df_hm_sc$row_label == "Node_13"]), 2.25)
expect_equal(unique(df_hm_sc$height[df_hm_sc$row_label == "Node_18"]), 8) ## scaled by 4
expect_equal(unique(df_hm_sc$height[df_hm_sc$row_label == "t8"]), 4)
expect_equal(unique(df_hm_sc$y[df_hm_sc$row_label == "Node_13"]), -0.9375)
for (n in rownames(ct)) {
for (m in colnames(ct)) {
expect_equal(df_hm_sc$value[df_hm_sc$variable == m &
df_hm_sc$row_label == n],
ct[n, m])
}
}
## Row names
df_rn <- getData(tree_hm = fig, type = "row_name")
expect_null(df_rn)
df_rn2 <- getData(tree_hm = figrn, type = "row_name")
expect_s3_class(df_rn2, "data.frame")
expect_equal(nrow(df_rn2), 7)
expect_equal(df_rn2$row_label[order(df_rn2$y)], c("t3", "Node_13", "t5",
"t10", "t1", "t8", "Node_18"))
expect_equal(unique(df_rn2$width), 0.6)
expect_equal(unique(df_rn2$x_right), 12.2)
expect_equal(unique(df_rn2$x_left), 6)
expect_equal(unique(df_rn2$x), 12.2)
## Column names
df_cn <- getData(tree_hm = fig, type = "column_name")
expect_s3_class(df_cn, "data.frame")
expect_equal(nrow(df_cn), 10)
expect_named(df_cn, c("variable", "x", "width", "y_top", "y_bottom", "y"))
expect_equal(diff(sort(df_cn$x)), c(rep(0.6, 4), 0.8, rep(0.6, 4)))
expect_equal(df_cn$variable, paste0("S", seq_len(10)))
expect_equal(unique(df_cn$y), 0.5)
expect_equal(unique(df_cn$y_top), 11.1)
expect_equal(unique(df_cn$y_bottom), 0.5)
expect_equal(unique(df_cn$width), 0.6)
## Title
df_title <- getData(tree_hm = fig, type = "title")
expect_s3_class(df_title, "data.frame")
expect_equal(df_title, data.frame(x = 9.1, y = 10.5, label = "First heatmap"))
## Column annotation
df_ca <- getData(tree_hm = fig, type = "column_anno")
expect_s3_class(df_ca, "data.frame")
expect_equal(nrow(df_ca), 10)
expect_named(df_ca, c("variable", "x", "width", "xend", "y", "yend",
"anno_group", "anno_color"))
expect_equal(df_ca$variable, paste0("S", seq_len(10)))
expect_equal(df_ca$x - df_cn$x, rep(-0.3, 10))
expect_equal(df_ca$x - df_ca$xend, rep(-0.6, 10))
expect_equal(df_ca$anno_group, rep(c("A", "B"), each = 5),
ignore_attr = TRUE)
expect_equal(df_ca$anno_color, rep(c("red", "blue"), each = 5),
ignore_attr = TRUE)
## Column order
df_cord <- getData(tree_hm = fig, type = "column_order")
expect_type(df_cord, "character")
## Samples are clustered
expect_equal(df_cord, c("S4", "S5", "S1", "S2", "S3",
"S6", "S7", "S10", "S8", "S9"))
## Column split
df_spl <- getData(tree_hm = fig, type = "column_split")
expect_s3_class(df_spl, "tbl_df")
expect_equal(nrow(df_spl), 2)
expect_named(df_spl, c("split_level", "x", "y", "column_split"))
expect_equal(df_spl$column_split, c("A", "B"))
})
fionarhuang/treeclimbR documentation built on Aug. 7, 2024, 12:44 p.m.
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test_that("getData works", {
## Generate some data
## -------------------------------------------------------------------------
library(TreeSummarizedExperiment)
library(ggtree)
library(ggplot2)
library(ggnewscale)
library(viridis)
library(dplyr)
data(tinyTree)
## Simulate data with 10 features and 10 samples (5 from each of 2 groups)
p1 <- c(rep(0.1/3, 3), rep(0.4/2, 2), rep(0.1, 5))
p2 <- c(rep(0.4/3, 3), rep(0.1/2, 2), rep(0.1, 5))
set.seed(1)
ct0 <- cbind(rmultinom(n = 5, size = 50, prob = p1),
rmultinom(n = 5, size = 50, prob = p2))
colnames(ct0) <- paste("S", seq_len(10), sep = "")
rownames(ct0) <- convertNode(tree = tinyTree, node = seq_len(10))
oo <- sample(seq_len(10))
ct0 <- ct0[, oo]
ct <- rbind(colSums(ct0[seq(1, 3), ]), colSums(ct0[seq(4, 5), ]),
ct0[seq(6, 10), ])
colnames(ct) <- paste("S", seq_len(10), sep = "")
rownames(ct) <- convertNode(tree = tinyTree, node = c(13, 18, seq(6, 10)))
col_split <- ifelse(colnames(ct) %in% paste0("S", seq_len(5)), "A", "B")
names(col_split) <- colnames(ct)
## Prepare the heatmaps
tree_fig <- ggtree(tinyTree, branch.length = "none",
layout = "rectangular", open.angle = 100) +
geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
geom_hilight(node = 13, fill = "blue", alpha = 0.3)
fig <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue"
)
## Figure with row names
figrn <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE
)
## Figure with scaled tree
tree_fig_sc <- ggtree(tinyTree, branch.length = "none",
layout = "rectangular", open.angle = 100)
tree_fig_sc <- ggtree::scaleClade(tree_fig_sc, node = 15, scale = 4)
tree_fig_sc <- ggtree::scaleClade(tree_fig_sc, node = 14, scale = 0.25) +
geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
geom_hilight(node = 13, fill = "blue", alpha = 0.3)
figsc <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig_sc, hm_data = ct,
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE, rownames_hjust = 0, rownames_offset_x = 0.1
)
## Provide column order -> ignore cluster_column
expect_warning({
figco <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
column_order = paste0("S", seq_len(10)),
cluster_column = TRUE, column_split = col_split,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE
)}, "column_order is ignored when column_split is given")
expect_warning({
figco <- TreeHeatmap(
tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
column_order = paste0("S", seq_len(10)),
cluster_column = TRUE, column_split = NULL,
column_anno = col_split, column_anno_gap = 0.6,
column_anno_color = c(A = "red", B = "blue"),
show_colnames = TRUE, colnames_position = "bottom",
colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
show_title = TRUE, title_offset_y = 1.5, title_color = "blue",
show_rownames = TRUE
)}, "cluster_column is ignored because column_order is given")
## Check that the function fails with wrong input
## -------------------------------------------------------------------------
expect_error(getData(tree_hm = 1, type = "heatmap"),
"'tree_hm' must be of class 'ggtree'")
expect_error(getData(tree_hm = fig, type = "missing"),
"'arg' should be one of")
## Check that the function works with correct input
## -------------------------------------------------------------------------
## Heatmap data
df_hm <- getData(tree_hm = fig, type = "heatmap")
expect_s3_class(df_hm, "data.frame")
expect_equal(nrow(df_hm), 70) ## 7 blocks, 10 samples
expect_named(df_hm, c("node", "row_label", "x", "y", "height", "width",
"variable", "value", "column_order", "split_level"))
expect_equal(df_hm$row_label, rep(rownames(ct), each = 10))
expect_equal(df_hm$column_order, rep(c(2, 3, 4, 0, 1, 5, 6, 8, 9, 7), 7))
expect_equal(df_hm$variable, factor(rep(paste0("S", seq_len(10)), 7),
levels = c("S4", "S5", "S1", "S2", "S3",
"S6", "S7", "S10", "S8",
"S9")))
expect_true(all(diff(df_hm$x[order(df_hm$column_order)]) >= 0))
expect_length(unique(paste(df_hm$column_order, df_hm$x)), 10)
expect_equal(unique(df_hm$width), 0.6)
expect_equal(unique(df_hm$split_level[df_hm$variable == "S1"]), 0)
expect_equal(unique(df_hm$split_level[df_hm$variable == "S8"]), 1)
expect_equal(unique(df_hm$height[df_hm$row_label == "Node_13"]), 3)
expect_equal(unique(df_hm$height[df_hm$row_label == "Node_18"]), 2)
expect_equal(unique(df_hm$height[df_hm$row_label == "t8"]), 1)
for (n in rownames(ct)) {
for (m in colnames(ct)) {
expect_equal(df_hm$value[df_hm$variable == m &
df_hm$row_label == n],
ct[n, m])
}
}
## ... from figure with row names
df_hm_rn <- getData(tree_hm = figrn, type = "heatmap")
expect_equal(df_hm, df_hm_rn)
## ... from figure with scaled tree
df_hm_sc <- getData(tree_hm = figsc, type = "heatmap")
expect_s3_class(df_hm_sc, "data.frame")
expect_equal(nrow(df_hm_sc), 70) ## 7 blocks, 10 samples
expect_named(df_hm_sc, c("node", "row_label", "x", "y", "height", "width",
"variable", "value", "column_order", "split_level"))
expect_equal(df_hm_sc$row_label, rep(rownames(ct), each = 10))
expect_equal(df_hm_sc$column_order, rep(c(2, 3, 4, 0, 1, 5, 6, 8, 9, 7), 7))
expect_equal(df_hm_sc$variable, factor(rep(paste0("S", seq_len(10)), 7),
levels = c("S4", "S5", "S1", "S2", "S3",
"S6", "S7", "S10", "S8",
"S9")))
expect_true(all(diff(df_hm_sc$x[order(df_hm_sc$column_order)]) >= 0))
expect_length(unique(paste(df_hm_sc$column_order, df_hm_sc$x)), 10)
expect_equal(unique(df_hm_sc$width), 0.6)
expect_equal(unique(df_hm_sc$split_level[df_hm_sc$variable == "S1"]), 0)
expect_equal(unique(df_hm_sc$split_level[df_hm_sc$variable == "S8"]), 1)
expect_equal(unique(df_hm_sc$height[df_hm_sc$row_label == "Node_13"]), 2.25)
expect_equal(unique(df_hm_sc$height[df_hm_sc$row_label == "Node_18"]), 8) ## scaled by 4
expect_equal(unique(df_hm_sc$height[df_hm_sc$row_label == "t8"]), 4)
expect_equal(unique(df_hm_sc$y[df_hm_sc$row_label == "Node_13"]), -0.9375)
for (n in rownames(ct)) {
for (m in colnames(ct)) {
expect_equal(df_hm_sc$value[df_hm_sc$variable == m &
df_hm_sc$row_label == n],
ct[n, m])
}
}
## Row names
df_rn <- getData(tree_hm = fig, type = "row_name")
expect_null(df_rn)
df_rn2 <- getData(tree_hm = figrn, type = "row_name")
expect_s3_class(df_rn2, "data.frame")
expect_equal(nrow(df_rn2), 7)
expect_equal(df_rn2$row_label[order(df_rn2$y)], c("t3", "Node_13", "t5",
"t10", "t1", "t8", "Node_18"))
expect_equal(unique(df_rn2$width), 0.6)
expect_equal(unique(df_rn2$x_right), 12.2)
expect_equal(unique(df_rn2$x_left), 6)
expect_equal(unique(df_rn2$x), 12.2)
## Column names
df_cn <- getData(tree_hm = fig, type = "column_name")
expect_s3_class(df_cn, "data.frame")
expect_equal(nrow(df_cn), 10)
expect_named(df_cn, c("variable", "x", "width", "y_top", "y_bottom", "y"))
expect_equal(diff(sort(df_cn$x)), c(rep(0.6, 4), 0.8, rep(0.6, 4)))
expect_equal(df_cn$variable, paste0("S", seq_len(10)))
expect_equal(unique(df_cn$y), 0.5)
expect_equal(unique(df_cn$y_top), 11.1)
expect_equal(unique(df_cn$y_bottom), 0.5)
expect_equal(unique(df_cn$width), 0.6)
## Title
df_title <- getData(tree_hm = fig, type = "title")
expect_s3_class(df_title, "data.frame")
expect_equal(df_title, data.frame(x = 9.1, y = 10.5, label = "First heatmap"))
## Column annotation
df_ca <- getData(tree_hm = fig, type = "column_anno")
expect_s3_class(df_ca, "data.frame")
expect_equal(nrow(df_ca), 10)
expect_named(df_ca, c("variable", "x", "width", "xend", "y", "yend",
"anno_group", "anno_color"))
expect_equal(df_ca$variable, paste0("S", seq_len(10)))
expect_equal(df_ca$x - df_cn$x, rep(-0.3, 10))
expect_equal(df_ca$x - df_ca$xend, rep(-0.6, 10))
expect_equal(df_ca$anno_group, rep(c("A", "B"), each = 5),
ignore_attr = TRUE)
expect_equal(df_ca$anno_color, rep(c("red", "blue"), each = 5),
ignore_attr = TRUE)
## Column order
df_cord <- getData(tree_hm = fig, type = "column_order")
expect_type(df_cord, "character")
## Samples are clustered
expect_equal(df_cord, c("S4", "S5", "S1", "S2", "S3",
"S6", "S7", "S10", "S8", "S9"))
## Column split
df_spl <- getData(tree_hm = fig, type = "column_split")
expect_s3_class(df_spl, "tbl_df")
expect_equal(nrow(df_spl), 2)
expect_named(df_spl, c("split_level", "x", "y", "column_split"))
expect_equal(df_spl$column_split, c("A", "B"))
})
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