From 4ca975bf810043ea31e8feff9c639f3733209090 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sun, 1 Nov 2020 16:46:42 +0000
Subject: [PATCH] added boxplot_stat.R to output plots for all sample types

---
 boxplot_stat.R | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 boxplot_stat.R

diff --git a/boxplot_stat.R b/boxplot_stat.R
new file mode 100644
index 0000000..b271c1d
--- /dev/null
+++ b/boxplot_stat.R
@@ -0,0 +1,71 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd("~/git/mosaic_2020/")
+getwd()
+###############################################################
+source("boxplot_stat_function.R")
+source("plot_data.R")
+#=============
+# Output:
+#=============
+outfile_bp = paste0("boxplots_stats_all", ".pdf")
+output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
+pdf(output_boxplot_stats, width=22, height=16)
+
+#===========================
+# NPA
+#===========================
+my_sample_npa = "NPA"
+plots_npa = doMyPlots(lf_fp_npa)
+npa_plot = ggpubr::ggarrange(plotlist = plots_npa
+                             , align = "hv"
+                             , ncol = 7
+                             , nrow = 5
+                             , common.legend = T)
+#npa_plot
+npa_plot_annot = annotate_figure(npa_plot
+                , top = text_grob(my_sample_npa, color = "blue", face = "bold", size = 14)
+                , bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
+                                   , color = "blue"
+                                   , hjust = 1, x = 0.98, face = "italic", size = 10)
+                , left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
+npa_plot_annot
+#dev.off()
+#===========================
+# SAM
+#===========================
+my_sample_sam = "SAM"
+plots_sam = doMyPlots(lf_fp_sam)
+sam_plot = ggpubr::ggarrange(plotlist = plots_sam
+                             , align = "hv"
+                             , ncol = 7
+                             , nrow = 5
+                             , common.legend = T)
+#sam_plot
+sam_plot_annot = annotate_figure(sam_plot
+                                 , top = text_grob(my_sample_sam, color = "blue", face = "bold", size = 14)
+                                 , bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
+                                                      , color = "blue"
+                                                      , hjust = 1, x = 0.98, face = "italic", size = 10)
+                                 , left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
+sam_plot_annot
+#dev.off()
+#===========================
+# SERUM 
+#===========================
+my_sample_serum = "serum"
+plots_serum = doMyPlots(lf_fp_serum)
+serum_plot = ggpubr::ggarrange(plotlist = plots_serum
+                               , align = "hv"
+                               , ncol = 7
+                               , nrow = 5
+                               , common.legend = T)
+#serum_plot
+serum_plot_annot = annotate_figure(serum_plot
+                                   , top = text_grob(my_sample_serum, color = "blue", face = "bold", size = 14)
+                                   , bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
+                                                        , color = "blue"
+                                                        , hjust = 1, x = 0.98, face = "italic", size = 10)
+                                   , left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
+serum_plot_annot
+dev.off()