added try catch for error handling
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9c141326aa
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8033c1785f
3 changed files with 69 additions and 54 deletions
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@ -7,7 +7,7 @@ getwd()
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# Input
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#=============
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source("boxplot_stat_function.R")
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source("boxplot_function.R") # for sam
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#source("boxplot_function.R") # for sam
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source("plot_data.R")
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#=============
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@ -23,10 +23,10 @@ pdf(output_boxplot_stats, width=22, height=16)
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#-------------
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# NPA
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#-------------
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my_sample_npa = "NPA"
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title_npa = "NPA"
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fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", my_sample_npa
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cat("\nPlotting boxplots with stats for:", title_npa
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, "\n========================================================\n")
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plots_npa = doMyPlotsStats(lf_fp_npa)
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@ -37,7 +37,7 @@ npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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, common.legend = T)
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#npa_plot
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npa_plot_annot = annotate_figure(npa_plot
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, top = text_grob(my_sample_npa
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, top = text_grob(title_npa
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, color = "blue"
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, face = "bold"
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, size = 18)
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@ -58,13 +58,14 @@ npa_plot_annot
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# FIXME: error handling!
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# For now, just calling plotting function without stats
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#-------------
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my_sample_sam = "SAM"
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title_sam = "SAM"
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fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
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cat("\nPlotting boxplots with stats for:", my_sample_sam
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cat("\nPlotting boxplots with stats for:", title_sam
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, "\n========================================================\n")
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plots_sam = doMyPlots(lf_fp_sam)
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#plots_sam = doMyPlots(lf_fp_sam)
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plots_sam = doMyPlotsStats(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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@ -72,7 +73,7 @@ sam_plot = ggpubr::ggarrange(plotlist = plots_sam
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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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, top = text_grob(title_sam
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, color = "blue"
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, face = "bold"
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, size = 18)
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@ -91,10 +92,10 @@ sam_plot_annot
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#-------------
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# SERUM
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#-------------
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my_sample_serum = "SERUM"
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title_serum = "SERUM"
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fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", my_sample_serum
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cat("\nPlotting boxplots with stats for:", title_serum
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, "\n========================================================\n")
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plots_serum = doMyPlotsStats(lf_fp_serum)
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@ -105,7 +106,7 @@ serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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, common.legend = T)
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#serum_plot
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serum_plot_annot = annotate_figure(serum_plot
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, top = text_grob(my_sample_serum
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, top = text_grob(title_serum
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, color = "blue"
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, face = "bold"
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, size = 18)
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@ -5,27 +5,30 @@ getwd()
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############################################################
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# TASK: boxplots with stats
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############################################################
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is.error <- function(x) inherits(x, "try-error")
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doMyPlotsStats <- function(df) {
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mediators = levels(as.factor(df$mediator))
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mediators = levels(as.factor(df$mediator))
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plots <- list()
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for (i in mediators) {
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cat("Creating plot for:", i, "\n")
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single=df[df$mediator==i,]
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plots <- list()
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max_y = max(single$value, na.rm = T)
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#cat("Plotting:", i, "max_y:", max_y, "\n")
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for (i in mediators) {
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cat("Plotting:", i, "\n")
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single=df[df$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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p = ggplot(single)+ 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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#----------
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# boxplot
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#----------
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p = ggplot(single)+ 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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@ -36,11 +39,14 @@ doMyPlotsStats <- function(df) {
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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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labs(title = i)
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#--------
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# stats
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#---------
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stats_state <- try({
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cat('Calculating stats for:', i, "\n")
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#--------
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# stats
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#---------
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stat_df <- single %>%
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group_by(timepoint, mediator) %>%
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wilcox_test(value ~ obesity, paired = F) %>%
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@ -49,17 +55,24 @@ doMyPlotsStats <- function(df) {
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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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plots[[i]] <- p2
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}, silent=TRUE)
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#print(stats_state)
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if ( is.error(stats_state)) {cat("⚠️ Stats ERROR:", i, "\n")}
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if ( ! is.error(stats_state)) {
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cat('Adding stats to plot for:', i, "\n")
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p = 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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}
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return(plots)
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plots[[i]] <- p
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}
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return(plots)
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}
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###############################################################
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27
boxplot_stat_log.R
Normal file → Executable file
27
boxplot_stat_log.R
Normal file → Executable file
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@ -7,12 +7,13 @@ getwd()
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# Input
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#=============
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source("boxplot_stat_function.R")
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source("boxplot_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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outfile_bp = paste0("boxplots_stats_all_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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@ -49,10 +50,10 @@ vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
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vl_temp_fix2$value[1:20]
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#------------------------------------------
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my_sample_npa = "NPA"
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title_npa = "NPA"
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fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
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cat("\nPlotting boxplots with stats for:", my_sample_npa
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cat("\nPlotting boxplots with stats for:", title_npa
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, "\n========================================================\n")
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plots_npa = doMyPlotsStats(lf_fp_npa)
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@ -63,10 +64,10 @@ npa_plot = ggpubr::ggarrange(plotlist = plots_npa
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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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, top = text_grob(title_npa
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, color = "blue"
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, face = "bold"
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, size = 14)
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, size = 18)
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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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@ -90,10 +91,10 @@ head(lf_fp_sam$value)
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lf_fp_sam$value = log10(lf_fp_sam$value)
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head(lf_fp_sam$value)
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my_sample_sam = "SAM"
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title_sam = "SAM"
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fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
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cat("\nPlotting boxplots with stats for:", my_sample_sam
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cat("\nPlotting boxplots with stats for:", title_sam
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, "\n========================================================\n")
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plots_sam = doMyPlots(lf_fp_sam)
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@ -104,10 +105,10 @@ sam_plot = ggpubr::ggarrange(plotlist = plots_sam
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, common.legend = T)
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#sam_plot
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sam_plot_annot = annotate_figure(sam_plot
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, top = text_grob(my_sample_sam
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, top = text_grob(title_sam
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, color = "blue"
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, face = "bold"
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, size = 14)
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, size = 18)
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, bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")")
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, color = "blue"
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, hjust = 1
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@ -131,10 +132,10 @@ head(lf_fp_serum$value)
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lf_fp_serum$value = log10(lf_fp_serum$value)
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head(lf_fp_serum$value)
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my_sample_serum = "serum"
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title_serum = "SERUM"
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fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
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cat("\nPlotting boxplots with stats for:", my_sample_serum
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cat("\nPlotting boxplots with stats for:", title_serum
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, "\n========================================================\n")
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plots_serum = doMyPlotsStats(lf_fp_serum)
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@ -145,10 +146,10 @@ serum_plot = ggpubr::ggarrange(plotlist = plots_serum
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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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, top = text_grob(title_serum
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, color = "blue"
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, face = "bold"
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, size = 14)
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, size = 18)
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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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