From c0d993b2327b36d48549d18953826ad91f1011f6 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sun, 1 Nov 2020 16:44:42 +0000
Subject: [PATCH] isolating function from running on data

---
 boxplot_stat_function.R | 52 +----------------------------------------
 1 file changed, 1 insertion(+), 51 deletions(-)

diff --git a/boxplot_stat_function.R b/boxplot_stat_function.R
index 085ed22..070adf9 100644
--- a/boxplot_stat_function.R
+++ b/boxplot_stat_function.R
@@ -26,7 +26,6 @@ doMyPlots <- function(df) {
                                            #, palette = c("#00BFC4", "#F8766D")
                                            ))+
         scale_colour_manual(values=c("#00BFC4", "#F8766D")) + 
-        scale_y_log10()
       theme(axis.text.x = element_text(size = 15)
             , axis.text.y = element_text(size = 15
                                          , angle = 0
@@ -50,7 +49,6 @@ doMyPlots <- function(df) {
       
       stat_df <- stat_df %>%
         add_xy_position(x = "timepoint", dodge = 0.8)
-      cat("printing p")
       p2 = p + stat_pvalue_manual(stat_df
                                    #, y.position = max_y
                                    , label = "{p_format} {p.signif}"
@@ -63,52 +61,4 @@ doMyPlots <- function(df) {
     return(plots)
   }
 
-###############################################################
-#============
-# test
-#============
-source("boxplot_linear.R")
-#=============
-# Output:
-#=============
-outfile_bp = paste0("boxplots_TEST", ".pdf")
-output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
-#pdf(output_boxplot_stats, width=22, height=16)
-
-med_names = c("eotaxin3", "il12p70", "itac", "il13")
-lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
-
-foo=doMyPlots(lf_test)
-#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
-baz
-#dev.off()
-##################################################################
-#=========================
-# entire sample_type data
-#=========================
-my_sample_type = "NPA"
-outfile_bp = paste0("boxplots_stats_", my_sample_type, ".pdf")
-output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
-pdf(output_boxplot_stats, width=22, height=16)
-
-#===========================
-# combine: ggpubr::ggarrange
-#===========================
-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_type, color = "purple", 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)
-                #, right = "I'm done, thanks :-)!",
-                #, fig.lab = "Figure 1", fig.lab.face = "bold"
-)
-npa_plot_annot
-dev.off()
+###############################################################
\ No newline at end of file