added boxplots with stats for non-severe analysis
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139
non_severe/boxplot_stat_linear.R
Executable file
139
non_severe/boxplot_stat_linear.R
Executable file
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#!/usr/bin/Rscript
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getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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###############################################################
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# TASK: boxplots with stats for NPA, SAM and SERUM
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# for each mediator, at each timepoint by group
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# TODO: check boxplot_stat_function.R
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# output plots even if stats fail due to data containing only LLODs
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# however for a given mediator, if there is error for ANY timepoint
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# stats will not be added for the entire plot! To be handled in
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# next iteration!
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###############################################################
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#=============
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# Input
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#=============
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source("boxplot_stat_function.R")
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source("plot_data_ns.R")
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#=============
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# Output
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#=============
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outfile_bp = paste0("boxplots_stats_all_NS-%03d.svg")
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output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
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svg(output_boxplot_stats, width=22, height=16)
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###############################################################
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#===============================
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# data assignment for plots
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#===============================
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table(lf_fp_npa$mediator)
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table(lf_fp_npa$T1_resp_score, lf_fp_npa$timepoint, lf_fp_npa$mediator == "eotaxin")
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#-------------
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# NPA
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#-------------
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title_npa = "NPA (non-severe)"
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fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", title_npa
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, "\n========================================================\n")
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plots_npa = doMyPlotsStats(lf_fp_npa)
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npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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, align = "hv"
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, ncol = 7
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, nrow = 5
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, common.legend = T)
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#npa_plot
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npa_plot_annot = annotate_figure(npa_plot
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, top = text_grob(title_npa
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, color = "blue"
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, face = "bold"
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFP non-severe adults (n=", fp_npa, ")")
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, color = "blue"
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, hjust = 1
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, x = 0.98
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, face = "italic"
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, size = 15)
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, left = text_grob("Levels (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 18))
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npa_plot_annot
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#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
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#-------------
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# SAM: NO STATS
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# FIXME: error handling!
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# For now, just calling plotting function without stats
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#-------------
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title_sam = "SAM (non-severe)"
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fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
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cat("\nPlotting boxplots with stats for:", title_sam
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, "\n========================================================\n")
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#plots_sam = doMyPlots(lf_fp_sam)
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plots_sam = doMyPlotsStats(lf_fp_sam)
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sam_plot = ggpubr::ggarrange(plotlist = plots_sam
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, align = "hv"
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, ncol = 7
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, nrow = 5
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, common.legend = T)
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#sam_plot
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sam_plot_annot = annotate_figure(sam_plot
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, top = text_grob(title_sam
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, color = "blue"
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, face = "bold"
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFP non-severe adults (n=", fp_sam, ")")
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, color = "blue"
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, hjust = 1
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, x = 0.98
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, face = "italic"
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, size = 15)
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, left = text_grob("Levels (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 18))
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sam_plot_annot
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#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
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#-------------
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# SERUM
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#-------------
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title_serum = "SERUM (non-severe)"
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fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", title_serum
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, "\n========================================================\n")
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plots_serum = doMyPlotsStats(lf_fp_serum)
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serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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, align = "hv"
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, ncol = 7
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, nrow = 5
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, common.legend = T)
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#serum_plot
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serum_plot_annot = annotate_figure(serum_plot
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, top = text_grob(title_serum
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, color = "blue"
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, face = "bold"
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFP non-severe adults (n=", fp_serum, ")")
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, color = "blue"
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, hjust = 1
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, x = 0.98
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, face = "italic"
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, size = 15)
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, left = text_grob("Levels (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 18))
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serum_plot_annot
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dev.off()
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###############################################################
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# END OF SCRIPT #
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###############################################################
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176
non_severe/boxplot_stat_log.R
Executable file
176
non_severe/boxplot_stat_log.R
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@ -0,0 +1,176 @@
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#!/usr/bin/Rscript
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getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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###############################################################
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# TASK: boxplots with stats for NPA, SAM and SERUM but with log scale
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# for each mediator, at each timepoint, by group
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# TODO: check boxplot_stat_function.R
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# output plots even if stats fail due to data containing only LLODs
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# however for a given mediator, if there is error for ANY timepoint
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# stats will not be added for the entire plot! To be handled in
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# next iteration!
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###############################################################
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#=============
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# Input
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#=============
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source("boxplot_stat_function.R")
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source("plot_data_ns.R")
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#=============
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# Output
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#=============
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outfile_bp = paste0("boxplots_stats_all_NS_LOG-%03d.svg")
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output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
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svg(output_boxplot_stats, width=22, height=16)
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###############################################################
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#===============================
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# data assignment for plots
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#===============================
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#----------------------------------------
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#-------
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# NPA
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#-------
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# vl data juggling with 0!
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vl_temp_fix = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
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vl_temp_fix$value[1:20]
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vl_temp_fix$value[vl_temp_fix$value == 0] <- 1
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vl_temp_fix$value[1:20]
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orig_nrow = nrow(lf_fp_npa); orig_nrow; table(lf_fp_npa$mediator)
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lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator=="vl_pfu_ul",]
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temp_nrow = nrow(lf_fp_npa); temp_nrow; table(lf_fp_npa$mediator)
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# add vl_temp_fix back
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lf_fp_npa = rbind(lf_fp_npa, vl_temp_fix)
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revised_nrow = nrow(lf_fp_npa); revised_nrow
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orig_nrow == revised_nrow
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head(lf_fp_npa$value)
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#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
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# log all values and reassign
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#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
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lf_fp_npa$value = log10(lf_fp_npa$value)
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head(lf_fp_npa$value)
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vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
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vl_temp_fix2$value[1:20]
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#------------------------------------------
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title_npa = "NPA (non-severe)"
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fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", title_npa
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, "\n========================================================\n")
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plots_npa = doMyPlotsStats(lf_fp_npa)
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npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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, align = "hv"
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, ncol = 7
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, nrow = 5
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, common.legend = T)
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#npa_plot
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npa_plot_annot = annotate_figure(npa_plot
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, top = text_grob(title_npa
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, color = "blue"
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, face = "bold"
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFP non-severe adults (n=", fp_npa, ")")
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, color = "blue"
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, hjust = 1
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, x = 0.98
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, face = "italic"
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, size = 15)
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, left = text_grob("Levels (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 18))
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npa_plot_annot
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#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
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#-------------
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# SAM
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#-------------
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head(lf_fp_sam$value)
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#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
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# log all values and reassign
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#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
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lf_fp_sam$value = log10(lf_fp_sam$value)
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head(lf_fp_sam$value)
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title_sam = "SAM (non-severe)"
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fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
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cat("\nPlotting boxplots with stats for:", title_sam
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, "\n========================================================\n")
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plots_sam = doMyPlotsStats(lf_fp_sam)
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sam_plot = ggpubr::ggarrange(plotlist = plots_sam
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, align = "hv"
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, ncol = 7
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, nrow = 5
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, common.legend = T)
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#sam_plot
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sam_plot_annot = annotate_figure(sam_plot
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, top = text_grob(title_sam
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, color = "blue"
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, face = "bold"
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFP non-severe adults (n=", fp_sam, ")")
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, color = "blue"
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, hjust = 1
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, x = 0.98
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, face = "italic"
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, size = 15)
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, left = text_grob("Levels (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 18))
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sam_plot_annot
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#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
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#------------------------------------------
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#-------------
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# SERUM
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#-------------
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head(lf_fp_serum$value)
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#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
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# log all values and reassign
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#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
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lf_fp_serum$value = log10(lf_fp_serum$value)
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head(lf_fp_serum$value)
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title_serum = "SERUM (non-severe)"
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fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", title_serum
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, "\n========================================================\n")
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plots_serum = doMyPlotsStats(lf_fp_serum)
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serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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, align = "hv"
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, ncol = 7
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, nrow = 5
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, common.legend = T)
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#serum_plot
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serum_plot_annot = annotate_figure(serum_plot
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, top = text_grob(title_serum
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, color = "blue"
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, face = "bold"
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFP non-severe adults (n=", fp_serum, ")")
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, color = "blue"
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, hjust = 1
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, x = 0.98
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, face = "italic"
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, size = 15)
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, left = text_grob("Levels (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 18))
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serum_plot_annot
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dev.off()
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###############################################################
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# END OF SCRIPT #
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###############################################################
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