tests/testthat/test-output.R

In jcooperdevlin/JoesFlow: Joes Flow simplified analysis for single cell modality data

# test functionality of tabular outputs

#########
# Setup #
#########

library(JoesFlow)
library(shiny)

# check which data sets we can test
extdata_dir  <- system.file( 'extdata', package = 'JoesFlow')
testData_dir <- system.file('testData', package = 'JoesFlow')

test_data <- tibble(lab = 'test',
                    flow = paste0(extdata_dir, '/flow.csv'),
                    meta = paste0(extdata_dir, '/metadata.csv'))

if(testData_dir != '')
{
  test_data <- tibble(lab = list.files(testData_dir),
                      flow = paste0(testData_dir, '/', lab, '/flow.csv'),
                      meta = paste0(testData_dir, '/', lab, '/metadata.csv')) %>%
    bind_rows(test_data)
}


#########
# Tests #
#########

test_that('Tabular output tests', {

  testServer(shinyApp(ui = app_ui(),
                      server = app_server),
             {
               # set up inputs
               session$setInputs(nav_bar                    = "Visualize",
                                 main_output                = 'UMAP',
                                 file1                      = NULL,
                                 file2                      = NULL,
                                 subsample                  = 0.2,
                                 seed                       = 247893,
                                 meta_val                   = "ID",
                                 clust_type                 = "Kmeans",
                                 kmean                      = 5,
                                 feat_dim                   = "PCA",
                                 colpal                     = "Default",
                                 show_hide_dimreduct_legend = "Show",
                                 show_hide_cluster_legend   = "Show",
                                 plot1_brush                = NULL,
                                 download_width             = 15,
                                 download_height            = 10)

               for(i in 1:nrow(test_data))
               {
                 # set input files (test_data_paths is a `reactiveValues` object in the app)
                 test_data_paths$flow <- test_data$flow[i]
                 test_data_paths$meta <- test_data$meta[i]


                 ### unit tests to run on all data sets ###

                 # check PCA output
                 tmp <- output$pca_coord_download %>%
                   read.table(sep = '\t', header = TRUE)

                 expect_s3_class(tmp, "data.frame")
                 expect_equal(names(tmp), c('SampleID', 'Group', 'cluster', 'PC1', 'PC2'))

                 # check UMAP output
                 tmp <- output$umap_coord_download %>%
                   read.table(sep = '\t', header = TRUE)

                 expect_s3_class(tmp, "data.frame")
                 expect_equal(names(tmp), c('SampleID', 'Group', 'cluster', 'UMAP_1', 'UMAP_2'))

                 # check tSNE output
                 tmp <- output$tsne_coord_download %>%
                   read.table(sep = '\t', header = TRUE)

                 expect_s3_class(tmp, "data.frame")
                 expect_equal(names(tmp), c('SampleID', 'Group', 'cluster', 'tSNE_1', 'tSNE_2'))

                 # check sample-based pca output
                 expect_s3_class(sb_vals(), 'tbl')
               }
             })
})