fix roxygenise deps; styler (#1183)

I had issues with running pre-commit due to bioc packages but those are
not needed at all!

.pre-commit-config.yaml

@@ -15,26 +15,32 @@ repos:
       - id: roxygenize
         name: Regenerate package documentation
         additional_dependencies:
+          - rtables
+          - broom
+          - car
           - checkmate
-          - digest
+          - cowplot
           - dplyr
+          - emmeans
+          - forcats
+          - formatters
           - ggplot2
-          - glue
-          - grDevices
+          - grid
+          - gridExtra
+          - gtable
+          - labeling
           - lifecycle
-          - logger
           - magrittr
+          - MASS
           - methods
-          - bioc::MultiAssayExperiment
-          - R6
+          - Rdpack
           - rlang
-          - rtables
-          - shinyjs
-          - shinyWidgets
+          - scales
           - stats
-          - bioc::SummarizedExperiment
+          - survival
+          - tibble
+          - tidyr
           - utils
-          - yaml
       - id: spell-check
         name: Check spelling with `spelling`
         exclude: >

DESCRIPTION

@@ -77,7 +77,7 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Collate:
     'formatting_functions.R'
     'abnormal.R'

R/bland_altman.R

@@ -85,18 +85,48 @@ g_bland_altman <- function(x, y, conf_level = 0.95) {
     geom_hline(yintercept = 0, color = "blue", linetype = 2) +
     geom_hline(yintercept = result_tem$lower_agreement_limit, color = "red", linetype = 2) +
     geom_hline(yintercept = result_tem$upper_agreement_limit, color = "red", linetype = 2) +
-    annotate("text", x = xpos, y = result_tem$lower_agreement_limit + 0.03 * yrange,
-             label = "lower limits of agreement", color = "red") +
-    annotate("text", x = xpos, y = result_tem$upper_agreement_limit + 0.03 * yrange,
-             label = "upper limits of agreement", color = "red") +
-    annotate("text", x = xpos, y = result_tem$difference_mean + 0.03 * yrange,
-             label = "mean of difference between two measures", color = "blue") +
-    annotate("text", x = xpos, y = result_tem$lower_agreement_limit - 0.03 * yrange,
-             label = sprintf("%.2f", result_tem$lower_agreement_limit), color = "red") +
-    annotate("text", x = xpos, y = result_tem$upper_agreement_limit - 0.03 * yrange,
-             label = sprintf("%.2f", result_tem$upper_agreement_limit), color = "red") +
-    annotate("text", x = xpos, y = result_tem$difference_mean - 0.03 * yrange,
-             label = sprintf("%.2f", result_tem$difference_meanm), color = "blue") +
+    annotate(
+      "text",
+      x = xpos,
+      y = result_tem$lower_agreement_limit + 0.03 * yrange,
+      label = "lower limits of agreement",
+      color = "red"
+    ) +
+    annotate(
+      "text",
+      x = xpos,
+      y = result_tem$upper_agreement_limit + 0.03 * yrange,
+      label = "upper limits of agreement",
+      color = "red"
+    ) +
+    annotate(
+      "text",
+      x = xpos,
+      y = result_tem$difference_mean + 0.03 * yrange,
+      label = "mean of difference between two measures",
+      color = "blue"
+    ) +
+    annotate(
+      "text",
+      x = xpos,
+      y = result_tem$lower_agreement_limit - 0.03 * yrange,
+      label = sprintf("%.2f", result_tem$lower_agreement_limit),
+      color = "red"
+    ) +
+    annotate(
+      "text",
+      x = xpos,
+      y = result_tem$upper_agreement_limit - 0.03 * yrange,
+      label = sprintf("%.2f", result_tem$upper_agreement_limit),
+      color = "red"
+    ) +
+    annotate(
+      "text",
+      x = xpos,
+      y = result_tem$difference_mean - 0.03 * yrange,
+      label = sprintf("%.2f", result_tem$difference_meanm),
+      color = "blue"
+    ) +
     xlab("Average of two measures") +
     ylab("Difference between two measures")