update tests and docs (#239)

Co-authored-by: m7pr <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Author: 3 people

R/draw_boxplot.R

@@ -88,7 +88,7 @@ draw_boxplot <- function(object,
     p + geom_boxplot(outlier.shape = ifelse(jitter, NA, 19)) +
       stat_boxplot(geom = "errorbar")
   } else {
-    p + geom_violin(draw_quantiles = c(0.75, 0.5, 0.25))
+    p + geom_violin(quantiles.linetype = c(0.75, 0.5, 0.25))
   }
   dodge_width <- ifelse(violin, 0.9, 0.75)
   jitter_width <- if (jitter) NULL else 0

tests/testthat/test-differential.R

@@ -128,12 +128,12 @@ test_that("autoplot for HermesDataDiffExpr works as expected with custom options
   dat <- hermes_data
   colData(dat) <- df_cols_to_factor(colData(dat))
   object <- diff_expression(dat, "SEX", "voom")
-  result <- autoplot(object, adj_p_val_thresh = 0.92, log2_fc_thresh = 3)
+  result <- autoplot(object, adj_p_val_thresh = 0.9206, log2_fc_thresh = 3)
 
   x <- layer_data(result, 1)
   x <- x[!is.na(x$label), ]
   expect_equal(x$x, c(-3.44, -3.19, 3.39, 3.21, 3.8, 3.12, -3.13), tolerance = 1e-2)
-  expect_equal(x$y, rep(0.04008, 7), tolerance = 1e-2)
+  expect_equal(x$y, rep(0.04, 7), tolerance = 5e-2)
   expect_identical(
     x$label,
     c(