114 lines
4 KiB
R
114 lines
4 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
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############################################################
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doMyPlots <- function(df) {
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mediators = levels(as.factor(df$mediator))
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plots <- list()
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for (i in mediators) {
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cat("Plotting:", i, "\n")
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single=df[df$mediator==i,]
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max_y = max(single$value, na.rm = T)
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cat("Plotting:", i, "max_y:", max_y, "\n")
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#----------
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# boxplot
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#----------
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p = ggplot(single)+ geom_boxplot(aes(x = timepoint
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, y = value
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, color = obesity
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#, palette = c("#00BFC4", "#F8766D")
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))+
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scale_colour_manual(values=c("#00BFC4", "#F8766D")) +
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scale_y_log10()
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theme(axis.text.x = element_text(size = 15)
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, axis.text.y = element_text(size = 15
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_blank()
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, axis.title.y = element_blank()
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, legend.position = "none"
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, plot.subtitle = element_text(size = 20, hjust = 0.5)
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, plot.title = element_text(size = 20, hjust = 0.5)) +
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labs(title = i)
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#--------
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# stats
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#---------
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stat_df <- single %>%
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group_by(timepoint, mediator) %>%
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wilcox_test(value ~ obesity, paired = F) %>%
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add_significance("p")
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stat_df$p_format = round(stat_df$p, digits = 3)
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stat_df <- stat_df %>%
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add_xy_position(x = "timepoint", dodge = 0.8)
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cat("printing p")
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p2 = p + stat_pvalue_manual(stat_df
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#, y.position = max_y
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, label = "{p_format} {p.signif}"
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, hide.ns = T
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, tip.length = 0)+
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scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
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plots[[i]] <- p2
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}
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return(plots)
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}
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###############################################################
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#============
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# test
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#============
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source("boxplot_linear.R")
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#=============
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# Output:
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#=============
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outfile_bp = paste0("boxplots_TEST", ".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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med_names = c("eotaxin3", "il12p70", "itac", "il13")
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lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
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foo=doMyPlots(lf_test)
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#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
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baz
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#dev.off()
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##################################################################
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#=========================
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# entire sample_type data
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#=========================
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my_sample_type = "NPA"
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outfile_bp = paste0("boxplots_stats_", my_sample_type, ".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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# combine: ggpubr::ggarrange
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#===========================
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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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, 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(my_sample_type, color = "purple", 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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#, right = "I'm done, thanks :-)!",
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#, fig.lab = "Figure 1", fig.lab.face = "bold"
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)
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npa_plot_annot
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dev.off()
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