added boxplot_stat_log.R to generate graphs with log data and stats
This commit is contained in:
parent
550e8b2c50
commit
b8ff7995ac
6 changed files with 249 additions and 10 deletions
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@ -28,7 +28,7 @@ fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", my_sample_npa
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cat("\nPlotting boxplots with stats for:", my_sample_npa
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, "\n========================================================\n")
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, "\n========================================================\n")
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plots_npa = doMyPlots(lf_fp_npa)
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plots_npa = doMyPlotsStats(lf_fp_npa)
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npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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, align = "hv"
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, align = "hv"
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, ncol = 7
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, ncol = 7
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@ -94,7 +94,7 @@ fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", my_sample_serum
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cat("\nPlotting boxplots with stats for:", my_sample_serum
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, "\n========================================================\n")
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, "\n========================================================\n")
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plots_serum = doMyPlots(lf_fp_serum)
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plots_serum = doMyPlotsStats(lf_fp_serum)
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serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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, align = "hv"
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, align = "hv"
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, ncol = 7
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, ncol = 7
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@ -5,7 +5,7 @@ getwd()
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############################################################
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############################################################
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# TASK: boxplots with stats
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# TASK: boxplots with stats
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############################################################
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############################################################
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doMyPlots <- function(df) {
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doMyPlotsStats <- function(df) {
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mediators = levels(as.factor(df$mediator))
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mediators = levels(as.factor(df$mediator))
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plots <- list()
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plots <- list()
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@ -61,4 +61,5 @@ doMyPlots <- function(df) {
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return(plots)
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return(plots)
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}
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}
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###############################################################
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###############################################################
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@ -22,8 +22,16 @@ pdf(output_boxplot_stats, width=22, height=16)
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#med_names = c("eotaxin3", "il12p70", "itac", "il13")
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#med_names = c("eotaxin3", "il12p70", "itac", "il13")
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#lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
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#lf_test = lf_fp_npa[lf_fp_npa$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=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
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foo_annot = annotate_figure(foo
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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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, top = text_grob(my_sample_name
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, color = "blue"
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, color = "blue"
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, face = "bold"
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, face = "bold"
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@ -41,3 +49,80 @@ foo_annot = annotate_figure(foo
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foo_annot
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foo_annot
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dev.off()
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dev.off()
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##################################################################
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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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153
boxplot_stat_log.R
Normal file
153
boxplot_stat_log.R
Normal file
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@ -0,0 +1,153 @@
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#!/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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#=============
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# Input
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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
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#=============
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outfile_bp = paste0("boxplots_stats_npa_serum_LOG", ".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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#===============================
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# data assignment for plots
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#===============================
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#----------------------------------------
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#-------
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# NPA
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#-------
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# vl data juggling with 0!
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vl_temp_fix = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
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vl_temp_fix$value[1:20]
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vl_temp_fix$value[vl_temp_fix$value == 0] <- 1
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vl_temp_fix$value[1:20]
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orig_nrow = nrow(lf_fp_npa); orig_nrow; table(lf_fp_npa$mediator)
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lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator=="vl_pfu_ul",]
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temp_nrow = nrow(lf_fp_npa); temp_nrow; table(lf_fp_npa$mediator)
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# add vl_temp_fix back
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lf_fp_npa = rbind(lf_fp_npa, vl_temp_fix)
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revised_nrow = nrow(lf_fp_npa); revised_nrow
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orig_nrow == revised_nrow
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head(lf_fp_npa$value)
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# log all values and reassign
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lf_fp_npa$value = log10(lf_fp_npa$value)
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head(lf_fp_npa$value)
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vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
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vl_temp_fix2$value[1:20]
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#------------------------------------------
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my_sample_npa = "NPA"
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fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", my_sample_npa
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, "\n========================================================\n")
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plots_npa = doMyPlotsStats(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_npa
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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(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")")
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, color = "blue"
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, hjust = 1
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, 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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npa_plot_annot
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#dev.off()
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#-------------
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# SAM
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#-------------
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#my_sample_sam = "SAM"
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#fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
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#cat("\nPlotting boxplots with stats for:", my_sample_sam
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# , "\n========================================================\n")
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#plots_sam = doMyPlots(lf_fp_sam)
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#sam_plot = ggpubr::ggarrange(plotlist = plots_sam
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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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#sam_plot_annot = annotate_figure(sam_plot
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# , top = text_grob(my_sample_sam
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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(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")")
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# , color = "blue"
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# , hjust = 1
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# , 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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#sam_plot_annot
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#dev.off()
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#------------------------------------------
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#-------------
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# SERUM
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#-------------
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head(lf_fp_serum$value)
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# reassign
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lf_fp_serum$value = log10(lf_fp_serum$value)
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head(lf_fp_serum$value)
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my_sample_serum = "serum"
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fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", my_sample_serum
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, "\n========================================================\n")
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plots_serum = doMyPlotsStats(lf_fp_serum)
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serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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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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#serum_plot
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serum_plot_annot = annotate_figure(serum_plot
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, top = text_grob(my_sample_serum
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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(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")")
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, color = "blue"
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, hjust = 1
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, 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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serum_plot_annot
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dev.off()
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###############################################################
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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("boxplot_linear.R")
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source("plot_data.R")
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#######################################################
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#######################################################
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med_names = c("eotaxin3", "il12p70", "itac", "il13")
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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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lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
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@ -21,7 +21,7 @@ metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
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#-----------
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#-----------
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# npa
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# npa
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#-----------
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#-----------
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#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
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wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
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lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
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lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
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lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
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lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
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lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
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lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
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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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#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
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wf_fp_sam = sam_wf[sam_wf$flustat == 1,]
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lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
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lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
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lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
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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$timepoint = as.factor(lf_fp_sam$timepoint)
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#-----------
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#-----------
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# serum
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# serum
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#-----------
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#-----------
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#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
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wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
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lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
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lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
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lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
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lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
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lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
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lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
|
||||||
|
|
|
||||||
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Add table
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Reference in a new issue