From 3b6776af24cc5d605d184ff43be28865bd821dda Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Fri, 20 Nov 2020 13:14:10 +0000 Subject: [PATCH] saving work --- boxplot_stat_linear.R | 16 ++++++++-------- boxplot_stat_log.R | 16 ++++++++-------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/boxplot_stat_linear.R b/boxplot_stat_linear.R index 9517258..b836d9c 100755 --- a/boxplot_stat_linear.R +++ b/boxplot_stat_linear.R @@ -17,12 +17,12 @@ getwd() # Input #============= source("boxplot_stat_function.R") -source("plot_data.R") +source("plot_data_na.R") #============= # Output #============= -outfile_bp = paste0("boxplots_stats_all-%03d.svg") +outfile_bp = paste0("boxplots_stats_all_NA-%03d.svg") output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats svg(output_boxplot_stats, width=22, height=16) ############################################################### @@ -32,7 +32,7 @@ svg(output_boxplot_stats, width=22, height=16) #------------- # NPA #------------- -title_npa = "NPA" +title_npa = "NPA (non-asthmatics)" fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa cat("\nPlotting boxplots with stats for:", title_npa @@ -50,7 +50,7 @@ npa_plot_annot = annotate_figure(npa_plot , color = "blue" , face = "bold" , size = 18) - , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")") + , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_npa, ")") , color = "blue" , hjust = 1 , x = 0.98 @@ -67,7 +67,7 @@ npa_plot_annot # FIXME: error handling! # For now, just calling plotting function without stats #------------- -title_sam = "SAM" +title_sam = "SAM (non-asthmatics)" fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam cat("\nPlotting boxplots with stats for:", title_sam @@ -86,7 +86,7 @@ sam_plot_annot = annotate_figure(sam_plot , color = "blue" , face = "bold" , size = 18) - , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")") + , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_sam, ")") , color = "blue" , hjust = 1 , x = 0.98 @@ -101,7 +101,7 @@ sam_plot_annot #------------- # SERUM #------------- -title_serum = "SERUM" +title_serum = "SERUM (non-asthmatics)" fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum cat("\nPlotting boxplots with stats for:", title_serum @@ -119,7 +119,7 @@ serum_plot_annot = annotate_figure(serum_plot , color = "blue" , face = "bold" , size = 18) - , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")") + , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_serum, ")") , color = "blue" , hjust = 1 , x = 0.98 diff --git a/boxplot_stat_log.R b/boxplot_stat_log.R index 528073c..8a53d36 100755 --- a/boxplot_stat_log.R +++ b/boxplot_stat_log.R @@ -17,12 +17,12 @@ getwd() # Input #============= source("boxplot_stat_function.R") -source("plot_data.R") +source("plot_data_na.R") #============= # Output #============= -outfile_bp = paste0("boxplots_stats_all_LOG-%03d.svg") +outfile_bp = paste0("boxplots_stats_all_NA_LOG-%03d.svg") output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats svg(output_boxplot_stats, width=22, height=16) ############################################################### @@ -59,7 +59,7 @@ vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",] vl_temp_fix2$value[1:20] #------------------------------------------ -title_npa = "NPA" +title_npa = "NPA (non-asthmatics)" fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa cat("\nPlotting boxplots with stats for:", title_npa @@ -77,7 +77,7 @@ npa_plot_annot = annotate_figure(npa_plot , color = "blue" , face = "bold" , size = 18) - , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")") + , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_npa, ")") , color = "blue" , hjust = 1 , x = 0.98 @@ -100,7 +100,7 @@ head(lf_fp_sam$value) lf_fp_sam$value = log10(lf_fp_sam$value) head(lf_fp_sam$value) -title_sam = "SAM" +title_sam = "SAM (non-asthmatics)" fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam cat("\nPlotting boxplots with stats for:", title_sam @@ -118,7 +118,7 @@ sam_plot_annot = annotate_figure(sam_plot , color = "blue" , face = "bold" , size = 18) - , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")") + , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_sam, ")") , color = "blue" , hjust = 1 , x = 0.98 @@ -141,7 +141,7 @@ head(lf_fp_serum$value) lf_fp_serum$value = log10(lf_fp_serum$value) head(lf_fp_serum$value) -title_serum = "SERUM" +title_serum = "SERUM (non-asthmatics)" fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum cat("\nPlotting boxplots with stats for:", title_serum @@ -159,7 +159,7 @@ serum_plot_annot = annotate_figure(serum_plot , color = "blue" , face = "bold" , size = 18) - , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")") + , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_serum, ")") , color = "blue" , hjust = 1 , x = 0.98