Nothing
test_that("props 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 all work usually
v1 = run_var_proportions(mx_obj,table="raw")
v2 = run_var_proportions(mx_obj,table="both")
v3 = run_var_proportions(mx_obj,table="both",save_models = TRUE)
expect_equal(is.null(v1$var_data),FALSE)
expect_equal(dim(v2$var_data)[1],12)
expect_equal(unique(v2$var_data$table),c("raw","normalized"))
expect_equal(is.null(v3$var_models),FALSE)
## test exists in list
expect_error(run_var_proportions(mx_obj,table="none"))
## metadata cols
mx_obj1 = mx_obj
mx_obj1$data = mx_obj$data[,-6]
expect_error(run_var_proportions(mx_obj1,table="both",metadata_cols="metadata1_vals"))
## formula overrides work
v4 = run_var_proportions(mx_obj,table="raw",formula_override = "(1|slide_id)")
v5 = run_var_proportions(mx_obj,table="raw",formula_override = "(1|slide_id)+metadata1_vals",metadata_cols = "metadata1_vals")
expect_equal(is.null(v4$var_data),FALSE)
expect_equal(is.null(v5$var_data),FALSE)
expect_error(run_var_proportions(mx_obj,table="raw",formula_override = "none"))
expect_error(run_var_proportions(mx_obj,table="raw",formula_override = rnorm(100)))
})
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