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Tanushree Tunstall 2020-11-20 13:14:10 +00:00
parent 0d591c46f5
commit 3b6776af24
2 changed files with 16 additions and 16 deletions
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16
boxplot_stat_linear.R
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@ -17,12 +17,12 @@ getwd()
# Input # Input
#============= #=============
source("boxplot_stat_function.R") source("boxplot_stat_function.R")
source("plot_data.R") source("plot_data_na.R")
#============= #=============
# Output # 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 output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
svg(output_boxplot_stats, width=22, height=16) svg(output_boxplot_stats, width=22, height=16)
############################################################### ###############################################################
@ -32,7 +32,7 @@ svg(output_boxplot_stats, width=22, height=16)
#------------- #-------------
# NPA # NPA
#------------- #-------------
title_npa = "NPA" title_npa = "NPA (non-asthmatics)"
fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
cat("\nPlotting boxplots with stats for:", title_npa cat("\nPlotting boxplots with stats for:", title_npa
@ -50,7 +50,7 @@ npa_plot_annot = annotate_figure(npa_plot
, color = "blue" , color = "blue"
, face = "bold" , face = "bold"
, size = 18) , 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" , color = "blue"
, hjust = 1 , hjust = 1
, x = 0.98 , x = 0.98
@ -67,7 +67,7 @@ npa_plot_annot
# FIXME: error handling! # FIXME: error handling!
# For now, just calling plotting function without stats # For now, just calling plotting function without stats
#------------- #-------------
title_sam = "SAM" title_sam = "SAM (non-asthmatics)"
fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
cat("\nPlotting boxplots with stats for:", title_sam cat("\nPlotting boxplots with stats for:", title_sam
@ -86,7 +86,7 @@ sam_plot_annot = annotate_figure(sam_plot
, color = "blue" , color = "blue"
, face = "bold" , face = "bold"
, size = 18) , 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" , color = "blue"
, hjust = 1 , hjust = 1
, x = 0.98 , x = 0.98
@ -101,7 +101,7 @@ sam_plot_annot
#------------- #-------------
# SERUM # SERUM
#------------- #-------------
title_serum = "SERUM" title_serum = "SERUM (non-asthmatics)"
fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
cat("\nPlotting boxplots with stats for:", title_serum cat("\nPlotting boxplots with stats for:", title_serum
@ -119,7 +119,7 @@ serum_plot_annot = annotate_figure(serum_plot
, color = "blue" , color = "blue"
, face = "bold" , face = "bold"
, size = 18) , 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" , color = "blue"
, hjust = 1 , hjust = 1
, x = 0.98 , x = 0.98

16
boxplot_stat_log.R
View file

@ -17,12 +17,12 @@ getwd()
# Input # Input
#============= #=============
source("boxplot_stat_function.R") source("boxplot_stat_function.R")
source("plot_data.R") source("plot_data_na.R")
#============= #=============
# Output # 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 output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
svg(output_boxplot_stats, width=22, height=16) 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] vl_temp_fix2$value[1:20]
#------------------------------------------ #------------------------------------------
title_npa = "NPA" title_npa = "NPA (non-asthmatics)"
fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
cat("\nPlotting boxplots with stats for:", title_npa cat("\nPlotting boxplots with stats for:", title_npa
@ -77,7 +77,7 @@ npa_plot_annot = annotate_figure(npa_plot
, color = "blue" , color = "blue"
, face = "bold" , face = "bold"
, size = 18) , size = 18)
, bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")") , bottom = text_grob(paste0("Mosaic data\nFP non-asthmatic adults (n=", fp_npa, ")")
, color = "blue" , color = "blue"
, hjust = 1 , hjust = 1
, x = 0.98 , x = 0.98
@ -100,7 +100,7 @@ head(lf_fp_sam$value)
lf_fp_sam$value = log10(lf_fp_sam$value) lf_fp_sam$value = log10(lf_fp_sam$value)
head(lf_fp_sam$value) head(lf_fp_sam$value)
title_sam = "SAM" title_sam = "SAM (non-asthmatics)"
fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
cat("\nPlotting boxplots with stats for:", title_sam cat("\nPlotting boxplots with stats for:", title_sam
@ -118,7 +118,7 @@ sam_plot_annot = annotate_figure(sam_plot
, color = "blue" , color = "blue"
, face = "bold" , face = "bold"
, size = 18) , 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" , color = "blue"
, hjust = 1 , hjust = 1
, x = 0.98 , x = 0.98
@ -141,7 +141,7 @@ head(lf_fp_serum$value)
lf_fp_serum$value = log10(lf_fp_serum$value) lf_fp_serum$value = log10(lf_fp_serum$value)
head(lf_fp_serum$value) head(lf_fp_serum$value)
title_serum = "SERUM" title_serum = "SERUM (non-asthmatics)"
fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
cat("\nPlotting boxplots with stats for:", title_serum cat("\nPlotting boxplots with stats for:", title_serum
@ -159,7 +159,7 @@ serum_plot_annot = annotate_figure(serum_plot
, color = "blue" , color = "blue"
, face = "bold" , face = "bold"
, size = 18) , 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" , color = "blue"
, hjust = 1 , hjust = 1
, x = 0.98 , x = 0.98