266 lines
8.2 KiB
R
266 lines
8.2 KiB
R
#!/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_ob_paper.R")
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# numbers
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table(vl_lf_plot_df$mosaic)
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length(unique(vl_lf_plot_df$mosaic))
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table(vl_lf_plot_df$obesity, vl_lf_plot_df$timepoint)
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table(vl_lf_plot_df$obesity, vl_lf_plot_df$timepoint, vl_lf_plot_df$mediator)
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length(unique(npa_lf_plot_df$mosaic))
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table(npa_lf_plot_df$obesity, npa_lf_plot_df$timepoint, npa_lf_plot_df$mediator)
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table(npa_lf_plot_df$mediator, npa_lf_plot_df$obesity, npa_lf_plot_df$timepoint)
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ob_grp_npa = npa_wf[npa_wf$obesity==1,]
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nob_grp_npa = npa_wf[npa_wf$obesity==0,]
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wilcox.test(ob_grp_npa$il1_npa1,
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nob_grp_npa$il1_npa1, paired = F)
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wilcox.test(ob_grp_npa$il1_npa2,
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nob_grp_npa$il1_npa2, paired = F)
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wilcox.test(ob_grp_npa$il6_npa1,
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nob_grp_npa$il6_npa1, paired = F)
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wilcox.test(ob_grp_npa$il6_npa2,
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nob_grp_npa$il6_npa2, paired = F)
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wilcox.test(ob_grp_npa$il8_npa1,
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nob_grp_npa$il8_npa1, paired = F)
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wilcox.test(ob_grp_npa$il8_npa2,
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nob_grp_npa$il8_npa2, paired = F)
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wilcox.test(ob_grp_npa$ip10_npa1,
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nob_grp_npa$ip10_npa1, paired = F)
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wilcox.test(ob_grp_npa$ip10_npa2,
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nob_grp_npa$ip10_npa2, paired = F)
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length(unique(serum_lf_plot_df$mosaic))
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table(serum_lf_plot_df$obesity, serum_lf_plot_df$timepoint, serum_lf_plot_df$mediator)
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table(serum_lf_plot_df$mediator, serum_lf_plot_df$obesity, serum_lf_plot_df$timepoint)
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#=============
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# Output
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#=============
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outdir_plots_paper = "/home/tanu/git/mosaic_2020/output/plots_paper/"
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#outfile_bp = paste0("boxplots_stats_paper-%03d.png")
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#output_boxplot_stats = paste0(outdir_plots_paper, outfile_bp); output_boxplot_stats
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#svg(output_boxplot_stats, width=22, height=16)
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#png(output_boxplot_stats, width = 11, height = 8, units = "in", res = 300)
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###############################################################
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#===============================
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# data assignment for plots
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#===============================
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#-------------
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# NPA: VL
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#-------------
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#linear
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cat("plotting for FP adult patients:",
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length(unique(vl_lf_plot_df$mosaic)))
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# linear : but data is not visible
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plots_npa_vl = doMyPlotsStats(vl_lf_plot_df)
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npa_plot_vl = ggpubr::ggarrange(plotlist = plots_npa_vl
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, align = "hv"
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#, legend = c(0.8,1)
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#, legend = "bottom"
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, common.legend = T)
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npa_plot_vl
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# log
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plots_npa_vl_log = doMyPlotsStats(vl_lf_plot_df_log)
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npa_plot_vl_log = ggpubr::ggarrange(plotlist = plots_npa_vl_log
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, align = "hv"
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, common.legend = T
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)
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npa_plot_vl_log
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############################################################
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mediator_order = c("IFN-α2a","IFN-β", "IFN-γ", "IL-1", "IL-6", "CXCL8", "CXCL10", "TNF-α")
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#-----------------------------
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# NPA: selected mediators
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#-----------------------------
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# linear
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plots_npa = doMyPlotsStats(npa_lf_plot_df, custom_order = mediator_order)
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npa_plot_1 = ggpubr::ggarrange(plotlist = plots_npa
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, align = "hv"
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, ncol = 8
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, nrow = 1
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, common.legend = T)
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npa_plot = annotate_figure(npa_plot_1,
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top = text_grob("NPA"
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, color = "black"
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#, face = "bold"
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, size = 14))
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# log
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plots_npa_log = doMyPlotsStats(npa_lf_plot_df_log, custom_order = mediator_order)
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npa_plot_log_1 = ggpubr::ggarrange(plotlist = plots_npa_log
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, align = "hv"
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, ncol = 8
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, nrow = 1
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, common.legend = T)
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npa_plot_log = annotate_figure(npa_plot_log_1,
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top = text_grob("NPA"
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, color = "black"
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#, face = "bold"
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, size = 14))
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npa_plot_log
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#-------------------------------
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# SERUM: selected mediators
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#--------------------------------
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# linear
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plots_serum = doMyPlotsStats(serum_lf_plot_df, custom_order = mediator_order)
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serum_plot_1 = ggpubr::ggarrange(plotlist = plots_serum
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, align = "hv"
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, ncol = 8
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, nrow = 1
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, common.legend = F
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)
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serum_plot = annotate_figure(serum_plot_1,
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top = text_grob("Serum"
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, color = "black"
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#, face = "bold"
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, size = 14))
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serum_plot
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# log
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plots_serum_log = doMyPlotsStats(serum_lf_plot_log, custom_order = mediator_order)
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serum_plot_log_1 = ggpubr::ggarrange(plotlist = plots_serum_log
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, align = "hv"
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, ncol = 8
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, nrow = 1
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, common.legend = F)
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serum_plot_log = annotate_figure(serum_plot_log_1,
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top = text_grob("Serum"
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, color = "black"
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#, face = "bold"
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, size = 14))
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serum_plot_log
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##############################################################
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##############################################################
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cat ("Outplots will be in:", outdir_plots_paper)
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#======================
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# Output: Linear graphs
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#======================
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# viral load: linear
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viral_load_annot = annotate_figure(
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npa_plot_vl
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, left = text_grob("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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png(paste0(outdir_plots_paper, "viral_load_linear"),
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width = 5,
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height = 5,
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units = "in",
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res = 300)
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viral_load_annot
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dev.off()
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# npa and serum mediators: linear
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outplot_linear = cowplot::plot_grid(
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npa_plot,
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serum_plot,
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nrow = 2,
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rel_heights = c(1.15,1)
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)
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outplot_linear_annot = annotate_figure(
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outplot_linear
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, left = text_grob("pg/ml"
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, color = "black"
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, rot = 90
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, size = 16)
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)
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png(paste0(outdir_plots_paper, "npa_serum_linear"),
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width = 18,
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height = 6,
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units = "in",
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res = 300)
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outplot_linear_annot
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dev.off()
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#======================
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# Output: Log graphs
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#======================
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# viral load: log
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viral_load_log_annot = annotate_figure(
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npa_plot_vl_log
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, left = text_grob("Log10 (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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png(paste0(outdir_plots_paper, "viral_load_log" ),
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width = 5,
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height = 5,
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units = "in",
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res = 300)
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viral_load_log_annot
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dev.off()
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# npa and serum mediators: log
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outplot_log = cowplot::plot_grid(
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npa_plot_log,
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serum_plot_log,
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nrow = 2,
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rel_heights = c(1.15,1)
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)
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outplot_log_annot = annotate_figure(
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outplot_log
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, left = text_grob("Log10 (pg/ml)"
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, color = "black"
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, rot = 90
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, size = 16)
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)
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png(paste0(outdir_plots_paper, "npa_serum_log"),
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width = 18,
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height = 6,
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units = "in",
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res = 300)
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outplot_log_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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