tests/testthat/test-monocle_module_heatmap.R

In whtns/seuratTools: Tools for Managing Seurat Objects

test_that("heatmap is ordered by pseudotime", {
    # load packages------------------------------
    library(tidyverse)
    library(shiny)
    library(shinydashboard)
    library(SingleCellExperiment)
    library(ggraph)
    library(formattable)
    library(clustree)
    devtools::load_all()
    library(Seurat)

    seu <- readRDS("~/single_cell_projects/integrated_projects/7_seq_04142020/output/seurat/unfiltered_seu.rds")

    # debug(convert_seu_to_cds)
    # debug(monocle3::preprocess_cds)
    # debug(monocle_module_heatmap)

    resolution <- 1.6

    cds <- convert_seu_to_cds(seu$gene, resolution = resolution)

    # cds <- convert_seu_to_cds(seu$transcript, resolution = resolution)

    cds <- learn_graph_by_resolution(cds,
        seu$gene,
        resolution = resolution
    )

    cds <- monocle3::order_cells(cds, root_cells = c("ds20170407_S442"))

    cds_pr_test_res <- monocle3::graph_test(cds, neighbor_graph = "principal_graph", cores = 4, expression_family = "negbinom")

    cds_pr_test_res %>%
        subset(q_value < 0.05) %>%
        dplyr::arrange(q_value) %>%
        dplyr::select(-status)

    test0 <- monocle_module_heatmap(cds, rownames(cds_pr_test_res), 1.6, collapse_rows = TRUE, group.by = "batch")

    test1 <- monocle_module_heatmap(cds, rownames(cds_pr_test_res), 1.6, collapse_rows = TRUE, group.by = "batch")

    test0$module_heatmap
})