renamed file
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ee35e1cb20
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5 changed files with 96 additions and 40 deletions
110
boxplot_stat_all.R
Normal file → Executable file
110
boxplot_stat_all.R
Normal file → Executable file
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@ -3,19 +3,31 @@ getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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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.R")
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#=============
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# Output:
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# Output
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#=============
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outfile_bp = paste0("boxplots_stats_all", ".pdf")
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output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
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pdf(output_boxplot_stats, width=22, height=16)
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#===========================
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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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# NPA
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#===========================
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#-------------
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my_sample_npa = "NPA"
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fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", my_sample_npa
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, "\n========================================================\n")
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plots_npa = doMyPlots(lf_fp_npa)
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npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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, align = "hv"
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@ -24,36 +36,64 @@ npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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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(my_sample_npa, color = "blue", face = "bold", size = 14)
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, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
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, top = text_grob(my_sample_npa
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, color = "blue"
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, hjust = 1, x = 0.98, face = "italic", size = 10)
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, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
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, face = "bold"
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, size = 14)
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, bottom = text_grob(paste0("Mosaic data\nFlu positive 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 = 10)
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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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#dev.off()
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#===========================
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#-------------
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# SAM
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#===========================
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my_sample_sam = "SAM"
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plots_sam = doMyPlots(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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#-------------
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#my_sample_sam = "SAM"
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#fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
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#cat("\nPlotting boxplots with stats for:", my_sample_sam
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# , "\n========================================================\n")
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#plots_sam = doMyPlots(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(my_sample_sam, color = "blue", face = "bold", size = 14)
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, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
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, color = "blue"
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, hjust = 1, x = 0.98, face = "italic", size = 10)
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, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
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sam_plot_annot
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#sam_plot_annot = annotate_figure(sam_plot
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# , top = text_grob(my_sample_sam
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# , color = "blue"
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# , face = "bold"
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# , size = 14)
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# , bottom = text_grob(paste0("Mosaic data\nFlu positive 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 = 10)
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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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#dev.off()
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#===========================
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#-------------
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# SERUM
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#===========================
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#-------------
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my_sample_serum = "serum"
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fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", my_sample_serum
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, "\n========================================================\n")
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plots_serum = doMyPlots(lf_fp_serum)
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serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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, align = "hv"
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@ -62,10 +102,20 @@ serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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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(my_sample_serum, color = "blue", face = "bold", size = 14)
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, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
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, top = text_grob(my_sample_serum
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, color = "blue"
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, hjust = 1, x = 0.98, face = "italic", size = 10)
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, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
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, face = "bold"
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, size = 14)
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, bottom = text_grob(paste0("Mosaic data\nFlu positive 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 = 10)
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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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0
boxplot_stat_function.R
Normal file → Executable file
0
boxplot_stat_function.R
Normal file → Executable file
15
boxplot_stat_test.R → boxplot_stat_function_test.R
Normal file → Executable file
15
boxplot_stat_test.R → boxplot_stat_function_test.R
Normal file → Executable file
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@ -11,6 +11,7 @@ source("plot_data.R")
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my_sample_name = "SAM"
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to_remove = c("ifna2a", "il29")
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lf_fp_sam2 = lf_fp_sam[!lf_fp_sam$mediator%in%to_remove,]
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lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
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foo = doMyPlots(lf_fp_sam2)
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@ -23,11 +24,19 @@ pdf(output_boxplot_stats, width=22, height=16)
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#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
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foo_annot = annotate_figure(foo
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, top = text_grob(my_sample_name, color = "blue", face = "bold", size = 14)
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, top = text_grob(my_sample_name
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, color = "blue"
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, face = "bold"
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, size = 14)
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, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
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, color = "blue"
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, hjust = 1, x = 0.98, face = "italic", size = 10)
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, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18)
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, hjust = 1, x = 0.98
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, face = "italic"
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, size = 10)
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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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)
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foo_annot
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dev.off()
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0
boxplot_with_stats.R
Normal file → Executable file
0
boxplot_with_stats.R
Normal file → Executable file
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plot_data.R
Normal file → Executable file
11
plot_data.R
Normal file → Executable file
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@ -6,7 +6,7 @@ getwd()
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# TASK: boxplots at T1
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# FIXME: currently not rendering, problem with NAs for stats?
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############################################################
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my_samples = "npa_sam_serum"
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#=============
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# Input
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#=============
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@ -15,12 +15,6 @@ source("data_extraction_formatting.R")
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# check: adult variable and age variable discrepancy!
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metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
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#=============
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# Output:
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#=============
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outfile_bp = paste0("boxplots_linear_", my_samples, ".pdf")
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output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
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#===============================
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# data assignment for plots
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#================================
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@ -36,6 +30,7 @@ lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)
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table(lf_fp_npa$mediator)
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head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
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lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
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table(lf_fp_npa$mediator)
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#-----------
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# sam
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@ -49,6 +44,7 @@ lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)
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table(lf_fp_sam$mediator)
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head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
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lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
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table(lf_fp_sam$mediator)
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#-----------
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# serum
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@ -59,4 +55,5 @@ lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
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lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
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lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
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head(lf_fp_sam$value[lf_fp_serum$mediator == "vitd"])
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########################################################################
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