begin data prep

3 files changed, 192 insertions, 0 deletions

diff --git a/scripts/data_prep.R b/scripts/data_prep.R
new file mode 100644
index 0000000..acd9977
--- /dev/null
+++ b/scripts/data_prep.R
@@ -0,0 +1,31 @@
+library(tidyverse)
+library(ggpubr)
+library(knitr)
+
+data_simon <- read_csv("../csv/simon_data_extra.csv", na = "NULL")
+data_mike <- read_csv("../csv/mike_repeat_visit.csv", na = "NULL")
+
+simon_wide <- data_simon %>%
+    group_by(donor_id) %>%
+    summarise(
+              dup = duplicated(data_name)
+              ) %>%
+    filter(dup)
+simon_wide
+
+dview <- data_simon %>%
+    group_by(donor_id) %>%
+    mutate(dup = duplicated(data_name)) %>%
+    filter(dup) %>%
+    arrange(data_name) %>%
+    filter(donor_id == 285 & data_name == "CD4_pos_T_cells") %>%
+    kable(format = "latex", booktabs = TRUE)
+
+%>%
+    rowid_to_column() %>%
+    pivot_wider(
+                id_cols = donor_id,
+                names_from = data_name,
+                values_from = data,
+    )
+simon_wide
diff --git a/scripts/data_prep_desc.R b/scripts/data_prep_desc.R
new file mode 100644
index 0000000..f0983ef
--- /dev/null
+++ b/scripts/data_prep_desc.R
@@ -0,0 +1,160 @@
+library(tidyverse)
+library(ggpubr)
+
+data_simon <- read_csv("../csv/simon_data_extra.csv", na = "NULL")
+data_mike <- read_csv("../csv/mike_repeat_visit.csv", na = "NULL")
+
+f <- function(x, height = 0.05) {
+    ans <- median(x)
+    data.frame(ymin = ans - height / 2, ymax = ans + height / 2, y = ans)
+}
+
+simon_year_class <- data_simon %>%
+    select(donor_id, year, outcome, hai_response) %>%
+    mutate(outcome = factor(outcome, levels = c(1, 0), labels = c("H", "L"))) %>%
+    mutate(year_flag = year) %>%
+    mutate(outcome_flag = outcome) %>%
+    group_by(year, outcome) %>%
+    summarise(
+        year_flag = year_flag,
+        outcome_flag = outcome_flag,
+        donor_id = donor_id,
+        response = hai_response
+    )
+simon_year_class
+
+
+xlabels <- simon_year_class %>%
+    group_map(
+        ~ {
+            rep(paste(.$outcome_flag[1], "\nn=(", length(unique(.$donor_id)), ")"), nrow(.))
+        }
+    )
+
+count_high_and_low <- data_simon %>%
+    group_by(outcome) %>%
+    summarise(
+              count = length(unique(donor_id))
+    )
+
+simon_plt <- simon_year_class %>%
+    ungroup() %>%
+    mutate(label = unlist(xlabels)) %>%
+    ggplot(aes(label, log2(response))) +
+    geom_violin(aes(fill = outcome, color = outcome), alpha = 0.2, show.legend = F) +
+    geom_boxplot(width = 0.1, show.legend = F) +
+    stat_summary(
+        fun.data = f, geom = "crossbar",
+        colour = NA, fill = "black", width = 0.3, alpha = 1.0
+    ) +
+    geom_point(aes(fill = outcome), color = "black", shape = 23, show.legend = F) +
+    facet_grid(cols = vars(year), scales = "free") +
+    theme_pubclean() +
+    labs(x = "", y = "Log2 HAI response difference", title = paste(
+        "Donor first visit data used in SIMON, total=(", length(unique(simon_year_class$donor_id)), ")",
+        ", high=(", count_high_and_low[2,2], ")", ", low=(", count_high_and_low[1,2],")"
+    ))
+
+mike_repeat_visits <- data_mike %>%
+    mutate(year_flag = year) %>%
+    group_by(donor_id, outcome) %>%
+    summarise(
+        count = length(unique(year_flag)),
+        outcome = unique(outcome)
+    ) %>%
+    arrange(donor_id) %>%
+    ungroup()
+mike_repeat_visits
+
+repeat_plt <- mike_repeat_visits %>%
+    transmute(
+              second = sum(count >= 1),
+              third = sum(count >= 2),
+              fourth = sum(count >= 3),
+              fifth = sum(count >= 5)
+    ) %>%
+    pivot_longer(
+                 names_to = "visit",
+                 values_to = "count",
+                 cols = everything()
+    ) %>%
+    slice(1:4, ) %>%
+    ggplot(aes(factor(visit, levels=c("second", "third", "fourth", "fifth")), count, fill = visit)) +
+    geom_bar(stat="identity", show.legend=F) +
+    labs(x = "Repeat visit number", y = "Number of donors") +
+    theme_pubclean()
+repeat_plt
+
+mike_second_visit <- data_mike %>%
+    group_by(donor_id) %>%
+    filter(year == min(year))
+mike_second_visit
+
+mike_second_visit_year_class <- mike_second_visit %>%
+    select(donor_id, year, outcome, hai_response) %>%
+    mutate(outcome = factor(outcome, levels = c(1, 0), labels = c("H", "L"))) %>%
+    mutate(year_flag = year) %>%
+    mutate(outcome_flag = outcome) %>%
+    group_by(year, outcome) %>%
+    summarise(
+        year_flag = year_flag,
+        outcome_flag = outcome_flag,
+        donor_id = donor_id,
+        response = hai_response
+    )
+
+
+xlabels_mike <- mike_second_visit_year_class %>%
+    group_map(
+        ~ {
+            rep(paste(.$outcome_flag[1], "\nn=(", length(unique(.$donor_id)), ")"), nrow(.))
+        }
+    )
+
+count_high_and_low_mike <- mike_second_visit %>%
+    group_by(outcome) %>%
+    summarise(
+              count = length(unique(donor_id))
+    )
+
+f <- function(x, height = 0.02) {
+    ans <- median(x)
+    data.frame(ymin = ans - height / 2, ymax = ans + height / 2, y = ans)
+}
+
+
+mike_plt <- mike_second_visit_year_class %>%
+    ungroup() %>%
+    mutate(label = unlist(xlabels_mike)) %>%
+    ggplot(aes(label, log2(response))) +
+    geom_violin(aes(fill = outcome, color = outcome), alpha = 0.2, show.legend = F) +
+    geom_boxplot(width = 0.1, show.legend = F) +
+    stat_summary(
+        fun.data = f, geom = "crossbar",
+        colour = NA, fill = "black", width = 0.3, alpha = 1.0
+    ) +
+    geom_point(aes(fill = outcome), color = "black", shape = 23, show.legend = F) +
+    facet_grid(cols = vars(year), scales = "free") +
+    theme_pubclean() +
+    labs(x = "", y = "Log2 HAI response difference", title = paste(
+        "Donor second visit data used in this work, total=(", length(unique(mike_second_visit_year_class$donor_id)), ")",
+        ", high=(", count_high_and_low_mike[2,2], ")", ", low=(", count_high_and_low_mike[1,2],")"
+    ))
+mike_plt
+
+bottom <- ggarrange(
+                    repeat_plt,
+                    mike_plt,
+                    ncol=2,
+                    widths=c(1,2),
+                    labels=c("B", "C")
+)
+
+whole <- ggarrange(
+                   simon_plt,
+                   bottom,
+                   nrow=2,
+                   heights=c(1,1),
+                   labels=c("A", "")
+                   )
+ggsave("../images/data_selection.png", whole, width = 2 * 15, height = 19, dpi=300, units = "cm")
diff --git a/scripts/visit_inconsistencies.R b/scripts/visit_inconsistencies.R
index c495d9f..df6628d 100644
--- a/scripts/visit_inconsistencies.R
+++ b/scripts/visit_inconsistencies.R
@@ -30,6 +30,7 @@ post_gmt_vec <- class_correct %>%
                   }
               }
     )
+
 post_gmt_vec
 
 post_gmt_vec <- unlist(post_gmt_vec)