testing boxplots
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1 changed files with 23 additions and 216 deletions
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@ -6,230 +6,37 @@ getwd()
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# TASK: boxplots at T1
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# TASK: boxplots at T1
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# FIXME: currently not rendering, problem with NAs for stats?
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# FIXME: currently not rendering, problem with NAs for stats?
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############################################################
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############################################################
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my_sample_type = "serum"
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#=============
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#=============
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# Input
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# Input
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#=============
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#=============
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source("data_extraction_formatting.R")
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source("boxplot_linear.R")
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# check: adult variable and age variable discrepancy!
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mediators = levels(as.factor(lf_test$mediator))
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metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
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#=============
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plots <- list()
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# Output:
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#=============
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outfile_bp = paste0("boxplots_", my_sample_type, ".pdf")
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output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
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#===============================
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for (i in mediators) {
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# data assignment for plots
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single=lf_test[lf_test$mediator==i,]
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#================================
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#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
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lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
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lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
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lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
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lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)
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table(lf_fp_npa$mediator)
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p2 = ggboxplot(single
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head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
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, x = "timepoint"
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lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
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, y = "value"
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, color = "obesity"
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, palette = c("#00BFC4", "#F8766D")
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)
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stat_npa2 <- single %>%
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group_by(timepoint, mediator) %>%
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wilcox_test(value ~ obesity, paired = F) %>%
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add_significance("p")
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stat_npa2
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#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
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stat_npa2 <- stat_npa2 %>%
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lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
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add_xy_position(x = "timepoint", dodge = 0.8)
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lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
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lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
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lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)
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table(lf_fp_sam$mediator)
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p2 = p2 + stat_pvalue_manual(stat_npa2
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head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
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, label = "{p} {p.signif}"
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lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
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, hide.ns=T
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, tip.length = 0)
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plots[[i]] <- p2
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#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
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lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
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lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
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lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
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lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
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########################################################################
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cat("Output plots will be in:", output_boxplot)
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pdf(output_boxplot, width = 20, height = 15)
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#=======================================================================
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# NPA
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#=======================================================================
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if (is.factor(lf_fp_npa$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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}
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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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# SAM
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#=======================================================================
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if (is.factor(lf_fp_sam$timepoint) && is.factor(lf_fp_sam$timepoint)){
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cat ("PASS: required groups are factors")
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}
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#------------------------------------------
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title_sam_linear = "Boxplot: sam (Linear)"
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#-----------------------------------------
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bxp_sam_linear <- ggboxplot(lf_fp_sam, 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_sam_linear
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, x = ""
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, y = "Levels")
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bxp_sam_linear
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#------------------------------------
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title_sam_log = "Boxplot: sam (Log)"
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#-----------------------------------
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bxp_sam_log <- ggboxplot(lf_fp_sam, 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_sam_log
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, x = ""
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, y = "Levels (Log)")
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bxp_sam_log
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#=======================================================================
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# SERUM
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#=======================================================================
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if (is.factor(lf_fp_serum$timepoint) && is.factor(lf_fp_serum$timepoint)){
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cat ("PASS: required groups are factors")
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}
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table(lf_fp_serum$mediator)
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#------------------------------------------
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title_serum_linear = "Boxplot: serum (Linear)"
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#-----------------------------------------
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bxp_serum_linear <- ggboxplot(lf_fp_serum, 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_serum_linear
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, x = ""
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, y = "Levels")
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bxp_serum_linear
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#------------------------------------
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title_serum_log = "Boxplot: serum (Log)"
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#-----------------------------------
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bxp_serum_log <- ggboxplot(lf_fp_serum, 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_serum_log
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, x = ""
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, y = "Levels (Log)")
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bxp_serum_log
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dev.off()
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#==========================================================================
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