Revision 2 hpc

CirculatoryHealth · Jul 12, 2022 · 32cdc36 · 32cdc36
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diff --git a/.gitignore b/.gitignore
@@ -11,6 +11,7 @@ core*
 *swp
 *swo
 _archive_/*
+.*
 
 # R files
 .Rproj.user

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 [![DOI](https://zenodo.org/badge/386120447.svg)](https://zenodo.org/badge/latestdoi/386120447)
 
 
-> This README and repository accompany the paper _"Penetrance and disease expression of (likely) pathogenic variants associated with inherited cardiomyopathies in the general population"_ by [Bourfiss M. *et al*. **medRxiv 2022**](https://doi.org/10.1101/2022.01.06.22268837).
+> This README and repository accompany the paper _"Prevalence and disease expression of pathogenic and likely pathogenic variants associated with inherited cardiomyopathies in the general population"_ by [Bourfiss M. *et al*. **medRxiv 2022**](https://doi.org/10.1101/2022.01.06.22268837).
 --------------
 
 # Content

diff --git a/src/Create_Figure5.R b/src/Create_Figure5.R
@@ -37,9 +37,9 @@ theme_set(my_theme())
 #     #2 -- Path to and name of the output file,
 #           for example /hpc/dhl_ec/mvanvugt/UKBB/results/figures/Figure5.pdf
 
-args = commandArgs(trailingOnly = TRUE)
-input    = args[1]
-output   = args[2]
+args   = commandArgs(trailingOnly = TRUE)
+input  = args[1]
+output = args[2]
 
 
 ## Loading files ---------------------------------------------------------------
@@ -56,7 +56,7 @@ ex <- c("LV", "RV")
 cmr <- df %>% select(starts_with("RV"), starts_with("LV"), contains("Wall_thickness"), 
                      contains("Ecc", ignore.case = FALSE), 
                      contains("Ell", ignore.case = FALSE)) %>% 
-select(-any_of(ex)) %>% names()
+    select(-any_of(ex)) %>% names()
 # Create df with only P- participants
 new <- df %>% select(f.eid, BSA, CM, Pheno, Sex, any_of(cmr)) %>% 
     filter(Pheno == "Non-Diagnosed") %>% 
@@ -68,19 +68,20 @@ new <- df %>% select(f.eid, BSA, CM, Pheno, Sex, any_of(cmr)) %>%
 # LVEF boxplot
 p1 <- ggplot(new, 
              aes(x = factor(CM, levels = c("Controls", "ACM", "DCM", "HCM"),
-                            labels = c("Controls G-P-", "ARVC G+P-", "DCM G+P-", 
-                                       "HCM G+P-")), 
+                            labels = c("Controls G-P-", "ARVC G+P-", 
+                                       "DCM G+P-", "HCM G+P-")), 
                  y = LVEF, fill = CM)) +
-geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
-             lwd = .2, fatten = .8) +
-labs(x = "Cardiomyopathy", y = "LVEF (%)") +
-# annotate("segment", x = c(1, 1, 3), xend = c(3, 1, 3),
-#          y = c(90, 88, 88), yend = c(90, 90, 90), lwd = .2) +
-# annotate("text", x = 2, y = 92, label = "p=0.009", size = 1) +
-scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
-                  values = c("#4cbd97", "#ffd167", "#168ab2", "#ef476f")) +
-theme(legend.position="none", text = element_text(size = 3),
-      line = element_line(size = .2))
+        geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
+                     lwd = .2, fatten = .8) +
+        labs(x = "Cardiomyopathy", y = "LVEF (%)") +
+        # annotate("segment", x = c(1, 1, 3), xend = c(3, 1, 3),
+        #          y = c(90, 88, 88), yend = c(90, 90, 90), lwd = .2) +
+        # annotate("text", x = 2, y = 92, label = "p=0.009", size = 1) +
+        scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
+                          values = c("#4cbd97", "#ffd167", "#168ab2", 
+                                     "#ef476f")) +
+        theme(legend.position="none", text = element_text(size = 3),
+              line = element_line(size = .2))
 
 # RVEF boxplot
 p1.1 <- ggplot(new, 
@@ -102,64 +103,68 @@ theme(legend.position="none", text = element_text(size = 3),
 # LVEDVi boxplot
 p2 <- ggplot(new, 
              aes(x = factor(CM, levels = c("Controls", "ACM", "DCM", "HCM"),
-                            labels = c("Controls G-P-", "ARVC G+P-", "DCM G+P-", 
-                                       "HCM G+P-")), 
+                            labels = c("Controls G-P-", "ARVC G+P-", 
+                                       "DCM G+P-", "HCM G+P-")), 
                  y = LVEDVi, fill = CM)) +
-geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
-             lwd = .2, fatten = .8) +
-labs(x = "Cardiomyopathy", y = "LVEDVi (ml/m2)") +
-scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
-                  values = c("#4cbd97", "#ffd167", "#168ab2", "#ef476f")) +
-theme(legend.position="none", text = element_text(size = 3),
-      line = element_line(size = .2))
+        geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
+                     lwd = .2, fatten = .8) +
+        labs(x = "Cardiomyopathy", y = "LVEDVi (ml/m2)") +
+        scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
+                          values = c("#4cbd97", "#ffd167", "#168ab2", 
+                                     "#ef476f")) +
+        theme(legend.position="none", text = element_text(size = 3),
+              line = element_line(size = .2))
 
 # RVEDVi boxplot
 p2.1 <- ggplot(new, 
                aes(x = factor(CM, levels = c("Controls", "ACM", "DCM", "HCM"),
-                              labels = c("Controls G-P-", "ARVC G+P-", "DCM G+P-", 
-                                         "HCM G+P-")), 
+                              labels = c("Controls G-P-", "ARVC G+P-", 
+                                         "DCM G+P-", "HCM G+P-")), 
                    y = RVEDVi, fill = CM)) +
-geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
-             lwd = .2, fatten = .8) +
-labs(x = "Cardiomyopathy", y = "RVEDVi (ml/m2)")  +
-# annotate("segment", x = c(1, 1, 3), xend = c(3, 1, 3),
-#          y = c(166, 160, 160), yend = c(166, 166, 166), lwd = .2) +
-# annotate("text", x = 2, y = 170, label = "p=0.048", size = 1) +
-scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
-                  values = c("#4cbd97", "#ffd167", "#168ab2", "#ef476f")) +
-theme(legend.position="none", text = element_text(size = 3),
-      line = element_line(size = .2))
+        geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
+                     lwd = .2, fatten = .8) +
+        labs(x = "Cardiomyopathy", y = "RVEDVi (ml/m2)")  +
+        # annotate("segment", x = c(1, 1, 3), xend = c(3, 1, 3),
+        #          y = c(166, 160, 160), yend = c(166, 166, 166), lwd = .2) +
+        # annotate("text", x = 2, y = 170, label = "p=0.048", size = 1) +
+        scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
+                          values = c("#4cbd97", "#ffd167", "#168ab2", 
+                                     "#ef476f")) +
+        theme(legend.position="none", text = element_text(size = 3),
+              line = element_line(size = .2))
 
 # Max Wall thickness boxplot
 p3 <- ggplot(new, 
              aes(x = factor(CM, levels = c("Controls", "ACM", "DCM", "HCM"),
-                            labels = c("Controls G-P-", "ARVC G+P-", "DCM G+P-", 
-                                       "HCM G+P-")), 
+                            labels = c("Controls G-P-", "ARVC G+P-", 
+                                       "DCM G+P-", "HCM G+P-")), 
                  y = Maximum_wall_thickness, fill = CM)) +
-geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
-             lwd = .2, fatten = .8) +
-labs(x = "Cardiomyopathy", y = "Maximum wall thickness (mm)") +
-scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
-                  values = c("#4cbd97", "#ffd167", "#168ab2", "#ef476f")) +
-theme(legend.position="none", text = element_text(size = 3),
-      line = element_line(size = .2))
+        geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
+                     lwd = .2, fatten = .8) +
+        labs(x = "Cardiomyopathy", y = "Maximum wall thickness (mm)") +
+        scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
+                          values = c("#4cbd97", "#ffd167", "#168ab2", 
+                                     "#ef476f")) +
+        theme(legend.position="none", text = element_text(size = 3),
+              line = element_line(size = .2))
 
 # Peak longitudinal strain boxplot
 p4 <- ggplot(new, 
              aes(x = factor(CM, levels = c("Controls", "ACM", "DCM", "HCM"),
-                            labels = c("Controls G-P-", "ARVC G+P-", "DCM G+P-", 
-                                       "HCM G+P-")), 
+                            labels = c("Controls G-P-", "ARVC G+P-", 
+                                       "DCM G+P-", "HCM G+P-")), 
                  y = peakEll4Ch, fill = CM)) +
-geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
-             lwd = .2, fatten = .8) +
-labs(x = "Cardiomyopathy", y = "Peak longitudinal strain (%)") +
-# annotate("segment", x = c(1, 1, 3), xend = c(3, 1, 3),
-#          y = c(-5, -7, -7), yend = c(-5, -5, -5), lwd = .2) +
-# annotate("text", x = 2, y = -4, label = "p=0.009", size = 1) +
-scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
-                  values = c("#4cbd97", "#ffd167", "#168ab2", "#ef476f")) +
-theme(legend.position="none", text = element_text(size = 3),
-      line = element_line(size = .2))
+        geom_boxplot(outlier.shape = 18, outlier.size = .4, alpha = 0.9, 
+                     lwd = .2, fatten = .8) +
+        labs(x = "Cardiomyopathy", y = "Peak longitudinal strain (%)") +
+        # annotate("segment", x = c(1, 1, 3), xend = c(3, 1, 3),
+        #          y = c(-5, -7, -7), yend = c(-5, -5, -5), lwd = .2) +
+        # annotate("text", x = 2, y = -4, label = "p=0.009", size = 1) +
+        scale_fill_manual(breaks = c("Controls", "ACM", "DCM", "HCM"),
+                          values = c("#4cbd97", "#ffd167", "#168ab2", 
+                                     "#ef476f")) +
+        theme(legend.position="none", text = element_text(size = 3),
+              line = element_line(size = .2))
 
 
 ## Combine and save figure -----------------------------------------------------
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ core* @@
     *swp
     *swo
     _archive_/*
+    .*
     # R files
     .Rproj.user
@@ Expand Down @@