# .libPaths("R/library") library(getopt) mycolor <-c("#E41A1C","#1E90FF","#FF8C00","#4DAF4A","#984EA3","#40E0D0","#FFC0CB","#00BFFF","#FFDEAD","#90EE90","#EE82EE","#00FFFF","#F0A3FF", "#0075DC","#993F00","#4C005C","#2BCE48","#FFCC99","#808080","#94FFB5","#8F7C00","#9DCC00","#C20088","#003380","#FFA405","#FFA8BB","#426600","#FF0010","#5EF1F2","#00998F","#740AFF","#990000","#FFFF00","#CD0000","#3A89CC","#769C30","#D99536","#7B0078","#BFBC3B","#6E8B3D","#00688B","#C10077","#CAAA76","#EEEE00","#458B00","#8B4513","#008B8B","#6E8B3D","#8B7D6B","#7FFF00","#CDBA96","#ADFF2F") mycolor <- rep(mycolor,20) ## Default settings day_format = FALSE date_breaks = '3 days' # waiver() this needs ggplot2 maybe date_labels = '%b-%d' # waiver() y_axis_lable = '' group_dir = '' plot_avg = FALSE ribbon = '' # 'sd' 'ci' 'se' conf_interval = 0.95 ylim_upper_border = 0.20 ylim_lower_border = 0.05 x_angle = 90 # x axis text direction fig_width = 10 fig_height = 5 legend_x = 0.5 legend_y = 0.99 legend_position= c(legend_x,legend_y) # 'right' horizontal_legend = TRUE if_legend = TRUE spec <- matrix( c("help","h",0,"logical", "help", "file_dir","f",1,"character","input time_series file", "output_dir","o",1,"character","output pdf file", "day_format","B",2,"logical","default F [T/F], if input date is day(ymd) or day-time(dmy_hm)", "date_breaks","Q",2,"character","default '3 days' breaks of x-axis dates", "date_labels","W",2,"character","default '%b-%d' format of x-axis dates", "y_axis_lable","Z",2,"character","default None, y axis label", "y_axis_lable_parse","M",2,"character","default None, y axis label(parsed) cannot! have spacing between non-expr ! usage aa_(m^3/m^3)", "group_dir","g",2,"character","group file", "plot_avg","Y",2,"logical","T/F, if plot by groups' average", "ribbon","R",1,"character","ribbon's type: sd se ci (standard deviation/error, confident interval)", "conf_interval","U",1,"double","default 0.95, if ribbon is ci, set ci", "ylim_upper_border","O",1,"double","default 0.20, ylim porportion to upper bound", "ylim_lower_border","P",1,"double","default 0.05, ylim porportion to lower bound", "ymin","C",1,"double","default auto, y axis minimal", "ymax","X",1,"double","default auto, y axis maximal", "x_angle","L",2,"integer","default 90, angle of the x-axis labels", "fig_width","K",2,"integer","default 10, width of fig", "fig_height","J",2,"integer","default 5, height of fig", "legend_x","H",2,"double","default 0.5 [0-1], legend position", "legend_y","G",2,"double","default 0.99 [0-1], legend position", "legend_position","F",2,"character","default not used, can be set as: [left right up bottom]", "horizontal_legend","D",2,"logical","default T [T/F], if legend is horizontal", "if_legend","V",2,"logical","T/F, if show legend" ),byrow=TRUE, ncol=5) opt <- getopt(spec=spec) if( !is.null(opt$help) || is.null(opt$file_dir) || is.null(opt$output_dir) ){ cat(paste(getopt(spec=spec, usage = T), "\n")) quit() } if(!is.null(opt$file_dir)){file_dir<-opt$file_dir} if(!is.null(opt$output_dir)){output_dir<-opt$output_dir} if(!is.null(opt$day_format)){day_format<-opt$day_format} if(!is.null(opt$date_breaks)){date_breaks<-opt$date_breaks} if(!is.null(opt$date_labels)){date_labels<-opt$date_labels} if(!is.null(opt$y_axis_lable)){y_axis_lable<-opt$y_axis_lable} if(!is.null(opt$y_axis_lable_parse)){y_axis_lable<-parse(text = opt$y_axis_lable_parse)} if(!is.null(opt$group_dir)){group_dir<-opt$group_dir} if(!is.null(opt$plot_avg)){plot_avg<-opt$plot_avg} if(!is.null(opt$ribbon)){ribbon<-opt$ribbon ; plot_avg = TRUE} # set plot_avg as TRUE if(!is.null(opt$conf_interval)){conf_interval<-opt$conf_interval} if(!is.null(opt$ylim_upper_border)){ylim_upper_border<-opt$ylim_upper_border} if(!is.null(opt$ylim_lower_border)){ylim_lower_border<-opt$ylim_lower_border} if(!is.null(opt$x_angle)){x_angle<-opt$x_angle} if(!is.null(opt$fig_width)){fig_width<-opt$fig_width} if(!is.null(opt$fig_height)){fig_height<-opt$fig_height} if(!is.null(opt$legend_x)){legend_x<-opt$legend_x} if(!is.null(opt$legend_y)){legend_y<-opt$legend_y} if(!is.null(opt$legend_position)){legend_position<-opt$legend_position} if(!is.null(opt$horizontal_legend)){horizontal_legend<-opt$horizontal_legend} if(!is.null(opt$if_legend)){if_legend<-opt$if_legend} ##############################Start library(lubridate) library(tidyr) library(ggplot2) library(Rmisc) library(dplyr) ## load data df = read.csv(file_dir,sep='\t',row.names = NULL,check.names=FALSE) colnames(df)[1] = 'time' if(day_format){df$time= as_datetime(ymd(df$time))}else{df$time= dmy_hm(df$time)} sample_list = colnames(df)[c(2:length(colnames(df)))] df = gather(df,key=SampleID,value=value, all_of(sample_list)) df$SampleID <- factor(df$SampleID,levels = sample_list) ## load group file ; check if inputs consists ; merge with df by the order of group if(group_dir != ''){ group = read.csv(group_dir,sep='\t',row.names = 1,fileEncoding = "UTF-8",check.names=FALSE) colnames(group) = c("Group") group$SampleID = rownames(group) if(identical(group$SampleID[order(group$SampleID)],sample_list[order(sample_list)])){ df = merge(group, df,by="SampleID",all=T) df$Group <- factor(df$Group,levels = unique(group$Group)) }else{ cat('Sample name not match!\n') quit() } } ## if plot_avg, caculate avg and ribbons if(group_dir != ''){if(plot_avg){ df = summarySE(df, "value", groupvars = c("Group","time"), na.rm = TRUE, conf.interval = conf_interval) df$ci = replace_na(df$ci,0) df$sd = replace_na(df$sd,0) df$se = replace_na(df$se,0) df$ci_upper = df$value + df$ci *0.5 df$ci_lower = df$value - df$ci *0.5 df$sd_upper = df$value + df$sd *0.5 df$sd_lower = df$value - df$sd *0.5 df$se_upper = df$value + df$se *0.5 df$se_lower = df$value - df$se *0.5 df$SampleID = df$Group }} ## ylim of plot y_range = max(df$value,na.rm = T) - min(df$value,na.rm = T) ymax = max(df$value,na.rm = T) + y_range*ylim_upper_border ymin = min(df$value,na.rm = T) - y_range*ylim_lower_border ## if ribbons if(group_dir != ''){if(plot_avg){if(ribbon != ''){ ribbon_lower = paste(ribbon,'_lower',sep='') ribbon_upper = paste(ribbon,'_upper',sep='') ## Update ylim ymax = max(max(df[ribbon_upper],na.rm = T),ymax,na.rm = T) ymin = min(min(df[ribbon_lower],na.rm = T),ymin,na.rm = T) }}} # if user set ylim if(!is.null(opt$ymin)){ymin<-opt$ymin} if(!is.null(opt$ymax)){ymax<-opt$ymax} # init plot settings if(group_dir != ''){ time_series_plot = ggplot(df, aes(x = time, y = value, colour = Group ,group = SampleID)) if(plot_avg){if(ribbon != ''){time_series_plot = time_series_plot + geom_ribbon(aes_string(ymin = ribbon_lower, ymax = ribbon_upper, colour = NULL, fill = "Group"),alpha = 0.3, na.rm = T, show.legend = F)}} }else{ time_series_plot = ggplot(df, aes(x = time, y = value, colour = SampleID)) } # Plot lines ; Set Theme time_series_plot = time_series_plot + geom_line() time_series_plot = time_series_plot + labs(x='Date', y=y_axis_lable, color = '') time_series_plot = time_series_plot + scale_x_datetime(date_breaks = date_breaks, date_labels = date_labels) time_series_plot = time_series_plot + scale_y_continuous(limits = c(ymin, ymax)) if(horizontal_legend){ my_guide_legend = guide_legend(byrow = T,direction='horizontal') }else{ my_guide_legend = guide_legend(byrow = F,direction='vertical') } time_series_plot = time_series_plot + scale_colour_manual(values = mycolor,guide = my_guide_legend) + scale_fill_manual(values = mycolor) time_series_plot = time_series_plot + theme_bw() time_series_plot = time_series_plot + theme( panel.grid=element_blank(), axis.text.x = element_text(angle = x_angle, hjust = 0.5, vjust = 0.5,color="black", size= 10),#, family = 'TT Times New Roman'), axis.text.y = element_text(hjust = 0.5, vjust = 0.5,color="black", size= 10),#, family = 'TT Times New Roman'), axis.title.x = element_text(color="black", size= 16),#, family = 'TT Times New Roman'), axis.title.y = element_text(color="black", size= 16),#, family = 'TT Times New Roman'), legend.justification=legend_position, legend.position= legend_position ) ## if show legend if(if_legend != TRUE){ time_series_plot= time_series_plot + theme(legend.position="none")} # Save Plot ggsave(time_series_plot, filename=output_dir,width=fig_width,height=fig_height)