101 lines
No EOL
3 KiB
R
101 lines
No EOL
3 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(x, title = "TEST") {
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mediators = levels(as.factor(x$mediator))
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plots <- list()
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for (i in mediators) {
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cat("Plotting:", i, "\n")
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single=x[x$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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p2 = ggboxplot(single
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, x = "timepoint"
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, y = "value"
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, color = "obesity"
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#, palette = c("blue", "red")
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, palette = c("#00BFC4", "#F8766D")) +
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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_npa2 <- 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_npa2
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stat_npa2 <- stat_npa2 %>%
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add_xy_position(x = "timepoint", dodge = 0.8)
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p2 = p2 + stat_pvalue_manual(stat_npa2
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#, y.position = max_y
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, label = "{p} {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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scale_x_discrete()
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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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# 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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bar=doMyPlots(lf_fp_npa)
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#bang=cowplot::plot_grid(plotlist=bar, align = 'hv', ncol=7, nrow=5)
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#bang
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dev.off() |