Nothing
test_that("validate params works",{
mx_obj = mx_dataset(data=mxnorm::mx_sample,
slide_id="slide_id",
image_id="image_id",
marker_cols=c("marker1_vals","marker2_vals","marker3_vals"),
metadata_cols=c("metadata1_vals"))
## validate parameters
mx_obj = mx_normalize(mx_data=mx_obj,
transform="log10",
method="ComBat")
## confirm both works
u1 = run_reduce_umap(mx_obj,table="raw",marker_list = c("marker1_vals","marker2_vals","marker3_vals"))
u2 = run_reduce_umap(mx_obj,table="both",marker_list = c("marker1_vals","marker2_vals","marker3_vals"))
expect_equal(is.null(u1$umap_data),FALSE)
expect_equal(dim(u2$umap_data)[1],6000)
## table exists in list
expect_error(validate_reduce_umap_params(mx_obj,table="test",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),1,NULL))
## marker cols
mx_obj1 = mx_obj
mx_obj1$data = mx_obj1$data[,-3]
expect_error(validate_reduce_umap_params(mx_obj1,table="raw",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),downsample_pct = 1,metadata_cols = NULL))
expect_error(validate_reduce_umap_params(mx_obj1,table="both",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),downsample_pct = 1,metadata_cols = NULL))
## meta cols in raw
mx_obj1 = mx_obj
mx_obj1$data = mx_obj$data[,-6]
expect_error(validate_reduce_umap_params(mx_obj1,table="raw",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),downsample_pct = 1,metadata_cols = "metadata1_vals"))
expect_error(validate_reduce_umap_params(mx_obj1,table="both",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),downsample_pct = 1,metadata_cols = "metadata1_vals"))
## downsample pct
expect_error(validate_reduce_umap_params(mx_obj,table="both",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),downsample_pct = 100,metadata_cols = "metadata1_vals"))
## catches Inf
mx_obj$norm_data[1,5] = Inf
expect_error(validate_reduce_umap_params(mx_obj,table="raw",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),1,NULL))
## catches incorrect dims
mx_obj$norm_data <- data.frame(matrix(rnorm(9),3,3))
expect_error(validate_reduce_umap_params(mx_obj,table="raw",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),1,NULL))
## normalized data exists when "normalized" or "both
expect_error(validate_reduce_umap_params(mx_obj[-6],table="normalized",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),1,NULL))
expect_error(validate_reduce_umap_params(mx_obj[-6],table="both",marker_list = c("marker1_vals","marker2_vals","marker3_vals"),1,NULL))
})
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