From d5693912bd9f4cf3c6e623afffb487576ffe88ef Mon Sep 17 00:00:00 2001
From: HannahVMeyer <hannah.v.meyer@googlemail.com>
Date: Thu, 5 Mar 2020 15:26:45 -0500
Subject: [PATCH] Analysis of FD values obtained from CT scans

---
 .../visualisation-CT-FD.R                     | 75 +++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 fractal-analysis-processing/visualisation-CT-FD.R

diff --git a/fractal-analysis-processing/visualisation-CT-FD.R b/fractal-analysis-processing/visualisation-CT-FD.R
new file mode 100644
index 0000000..65c6f31
--- /dev/null
+++ b/fractal-analysis-processing/visualisation-CT-FD.R
@@ -0,0 +1,75 @@
+#################
+## libraries ####
+#################
+options(bitmapType = 'cairo', device = 'pdf')
+
+
+modules::import_package('tidyverse', attach=TRUE)
+modules::import_package('optparse', attach=TRUE)
+
+#################################
+## parameters and input data ####
+#################################
+option_list <- list(
+    make_option(c("-d", "--dir"), action="store", dest="dir",
+                type="character", help="Path to output directory
+                data [default: %default].", default=NULL),
+    make_option(c("--dcm"), action="store", dest="dcm",
+                type="character", help="Path to file with DCM per slice FD
+                [default: %default].", default=NULL),
+    make_option(c("-i", "--interpolate"), action="store", dest="interpolate",
+                type="integer", help="Number of slices to interpolate to
+               [default: %default].", default=9),
+    make_option(c("--ukb"), action="store", dest="ukb",
+                type="character", help="Path to file with UKB per slice FD
+                [default: %default].", default=NULL),
+    make_option(c("--debug"), action="store_true",
+                dest="debug", default=FALSE, type="logical",
+                help="If set, predefined arguments are used to test the script
+               [default: %default].")
+)
+
+args <- optparse$parse_args(OptionParser(option_list=option_list))
+
+if (args$debug) {
+    args <- list()
+    args$dir <- "~/data/ukbb/ukb-hrt/phenotypes"
+    args$ct <- "~/data/ukbb/ukb-hrt/rawdata/ct_fd.csv"
+    args$interpolate <- 9
+#############
+## data  ####
+#############
+
+## CT FD measurements ####
+FDalongHeart <-  read_csv(file.path(args$ct))
+colnames(FDalongHeart) <- c("ID", "Slice", "FD")
+FDalongHeart <- FDalongHeart %>% drop_na()
+
+################
+## analysis ####
+################
+
+# plot distribution of FD along heart
+FDalongHeart$Slice <- as.factor(FDalongHeart$Slice)
+FDalongHeart$Location <- "Apical section"
+FDalongHeart$Location[as.numeric(FDalongHeart$Slice) <= 3] <- "Basal section"
+FDalongHeart$Location[as.numeric(FDalongHeart$Slice) <= 6 &
+                          as.numeric(FDalongHeart$Slice) > 3] <- "Mid section"
+FDalongHeart$Location <- factor(FDalongHeart$Location,
+                               levels=c("Basal section", "Mid section",
+                                         "Apical section"))
+
+
+p_fd <- ggplot(data=FDalongHeart, aes(x=Slice, y=FD))
+p_fd <- p_fd +
+    geom_boxplot(aes(color=Location), outlier.size = 0.2) +
+    scale_color_manual(values=c('#67a9cf','#1c9099','#016c59')) +
+    labs(x="Slice", y="FD") +
+    theme_bw()
+
+ggsave(plot=p_fd,
+       file=paste(args$dir, "/FDAlongHeart_CT_all_slices",
+                  args$interpolate, ".pdf", sep=""),
+       height=2, width=5, units="in")
+
+