ploting npa before sam and serum for boxplots
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1 changed files with 63 additions and 81 deletions
144
boxplot.R
144
boxplot.R
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@ -46,6 +46,68 @@ lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
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cat("Output plots will be in:", output_boxplot)
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cat("Output plots will be in:", output_boxplot)
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pdf(output_boxplot, width = 20, height = 15)
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pdf(output_boxplot, width = 20, height = 15)
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#=======================================================================
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# NPA
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#=======================================================================
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if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
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cat ("PASS: required groups are factors")
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}
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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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#------------------------------------------
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title_npa_linear = "Boxplot: NPA (Linear)"
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#-----------------------------------------
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bxp_npa_linear <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value",
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color = "obesity", palette = c("#00BFC4", "#F8766D")) +
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facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
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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_text(size = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, legend.direction = "horizontal") +
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labs(title = title_npa_linear
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, x = ""
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, y = "Levels")
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bxp_npa_linear
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#------------------------------------
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title_npa_log = "Boxplot: NPA (Log)"
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#-----------------------------------
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bxp_npa_log <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value",
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color = "obesity", palette = c("#00BFC4", "#F8766D")) +
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facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = F)+
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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_text(size = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, legend.direction = "horizontal") +
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labs(title = title_npa_log
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, x = ""
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, y = "Levels (Log)")
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bxp_npa_log
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#=======================================================================
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#=======================================================================
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# SAM
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# SAM
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#=======================================================================
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#=======================================================================
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@ -164,87 +226,7 @@ bxp_serum_log <- ggboxplot(lf_fp_serum, x = "timepoint", y = "value",
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, x = ""
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, x = ""
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, y = "Levels (Log)")
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, y = "Levels (Log)")
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bxp_serum_log
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bxp_serum_log
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#=======================================================================
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# NPA
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#=======================================================================
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if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
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cat ("PASS: required groups are factors")
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}
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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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#------------------------------------------
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title_npa_linear = "Boxplot: NPA (Linear)"
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#-----------------------------------------
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bxp_npa_linear <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value",
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color = "obesity", palette = c("#00BFC4", "#F8766D")) +
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facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
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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_text(size = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, legend.direction = "horizontal") +
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labs(title = title_npa_linear
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, x = ""
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, y = "Levels")
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bxp_npa_linear
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#------------------------------------
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title_npa_log = "Boxplot: NPA (Log)"
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#-----------------------------------
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bxp_npa_log <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value",
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color = "obesity", palette = c("#00BFC4", "#F8766D")) +
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facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = F)+
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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_text(size = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, legend.direction = "horizontal") +
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labs(title = title_npa_log
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, x = ""
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, y = "Levels (Log)")
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bxp_npa_log
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dev.off()
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dev.off()
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#==========================================================================
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#==========================================================================
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#------------------------------------
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title_npa_log_stats = "Boxplot: NPA (Log) + stats"
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#-----------------------------------
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stat.test <- lf_fp_npa %>%
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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.test
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stat.test <- stat.test %>%
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add_xy_position(x = "timepoint", dodge = 0.8)
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bxp_npa_linear + stat_pvalue_manual(stat.test, label = "p.signif", tip.length = 0)
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bxp_npa_log + stat_pvalue_manual(stat.test, label = "p.signif", tip.length = 0)
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dev.off()
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