sample_code.R

# パッケージ読み込み ---------------------------------------------------------------
# パッケージをインストールしていない場合は各行のコメントアウトを実行

library(tidyverse)  # install.packages("tidyverse")
library(ggconsort)  # install.packages("remotes"); remotes::install_github("tgerke/ggconsort")
library(ggtext)  # install.packages("ggtext")
library(export)  # install.packages("remotes"); remotes::install_github("tomwenseleers/export")


# サンプルデータ -----------------------------------------------------------------

head(trial_data)


# 患者数カウントとラベル付け -----------------------------------------------------------

study_cohorts <- trial_data %>%
  cohort_start("Assessed for eligibility") %>%
  # Define cohorts using named expressions --------------------
# Notice that you can use previously defined cohorts in subsequent steps
cohort_define(
  consented = .full %>% filter(declined != 1),
  consented_chemonaive = consented %>% filter(prior_chemo != 1),
  randomized = consented_chemonaive %>% filter(bone_mets != 1),
  treatment_a = randomized %>% filter(treatment == "Drug A"),
  treatment_b = randomized %>% filter(treatment == "Drug B"),
  # anti_join is useful for counting exclusions -------------
  excluded = anti_join(.full, randomized, by = "id"),
  excluded_declined = anti_join(.full, consented, by = "id"),
  excluded_chemo = anti_join(consented, consented_chemonaive, by = "id"),
  excluded_mets = anti_join(consented_chemonaive, randomized, by = "id")
) %>%
  # Provide text labels for cohorts ---------------------------
cohort_label(
  consented = "Consented",
  consented_chemonaive = "Chemotherapy naive",
  randomized = "Randomized",
  treatment_a = "Allocated to arm A",
  treatment_b = "Allocated to arm B",
  excluded = "Excluded",
  excluded_declined = "Declined to participate",
  excluded_chemo = "Prior chemotherapy",
  excluded_mets = "Bone metastasis"
)

# サブコホートが一覧表示される
study_cohorts %>% 
  summary()


# 図のレイアウトとデザイン ------------------------------------------------------------

study_consort <- study_cohorts %>%
  consort_box_add(
    "full", 0, 50, cohort_count_adorn(study_cohorts, .full)
  ) %>%
  consort_box_add(
    "exclusions", 20, 40, glue::glue(
      '{cohort_count_adorn(study_cohorts, excluded)}<br>
      • {cohort_count_adorn(study_cohorts, excluded_declined)}<br>
      • {cohort_count_adorn(study_cohorts, excluded_chemo)}<br>
      • {cohort_count_adorn(study_cohorts, excluded_mets)}
      ')
  ) %>%
  consort_box_add(
    "randomized", 0, 30, cohort_count_adorn(study_cohorts, randomized)
  ) %>%
  consort_box_add(
    "arm_a", -30, 10, cohort_count_adorn(study_cohorts, treatment_a)
  ) %>%
  consort_box_add(
    "arm_b", 30, 10, cohort_count_adorn(study_cohorts, treatment_b)
  ) %>%
  consort_arrow_add(
    end = "exclusions", end_side = "left", start_x = 0, start_y = 40
  ) %>%
  consort_arrow_add(
    "full", "bottom", "randomized", "top"
  ) %>% 
  consort_arrow_add(
    start_x = 0, start_y = 30, end_x = 0, end_y = 20,
  ) %>%
  consort_line_add(
    start_x = -30, start_y = 20, end_x = 30, end_y = 20,
  ) %>% 
  consort_arrow_add(
    end = "arm_a", end_side = "top", start_x = -30, start_y = 20
  ) %>%
  consort_arrow_add(
    end = "arm_b", end_side = "top", start_x = 30, start_y = 20
  )


# フローチャートの表示・出力 --------------------------------------------------------------

# 表示
study_fig <- study_consort %>%
  ggplot() + 
  geom_consort() +
  theme_consort(margin_h = 8, margin_v = 1) +
  # you can include other ggplot geoms, as needed -------------
ggtext::geom_richtext(
  aes(x = 0, y = 10, label = "Allocation"),
  fill = "#9bc0fc"
)

study_fig

# パワーポイントに出力
export::graph2ppt(study_fig, file = "flowchart.pptx")


# サブコホートのデータフレームを引き出す ------------------------------------------------------------

study_cohorts %>%
  cohort_pull(.full)

study_cohorts %>%
  cohort_pull(randomized)