128 lines
4.2 KiB
R
Executable file
128 lines
4.2 KiB
R
Executable file
#!/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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source("boxplot_stat_function.R")
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source("plot_data.R")
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#=============
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# Output TEST
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#=============
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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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outfile_bp = paste0("boxplots_TEST_", my_sample_name, ".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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baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
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baz
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sam_plot = ggpubr::ggarrange(plotlist = foo
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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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foo_annot = annotate_figure(sam_plot
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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
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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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##################################################################
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# ind components of function
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my_sample_name = "SAM"
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to_remove = c("ifna2a"
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, "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$mediator%in%to_remove,]
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df_test = lf_fp_sam3
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df_test = lf_fp_sam2
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table(df_test$mediator)
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p = ggplot(df_test)+ 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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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 = "TEST")
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p
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#--------
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# stats
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#---------
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to_remove = c("ifna2a"
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, "il29")
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lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
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lf_fp_sam4 = lf_fp_sam3[lf_fp_sam3$timepoint == "t3",]
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table(lf_fp_sam4$timepoint)
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wilcox_test(value~obesity, data = lf_fp_sam4)
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table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
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time = c("t3")
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lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$timepoint%in%time,]
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table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
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med = c("il29")
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time2 = c("t2")
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lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$mediator%in%med && lf_fp_sam3$timepoint%in%time2,]
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table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
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df_test = lf_fp_sam3
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table(df_test$mediator)
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stat_df <- df_test %>%
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group_by(timepoint, mediator) %>%
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wilcox_test(value ~ obesity, paired = F) %>%
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add_significance("p")
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stat_df$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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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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p2
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