added loess data in read_data.R and plotting scripts for loess
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5 changed files with 716 additions and 8 deletions
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loess_plots_days_into_hospitalisation.R
Executable file
226
loess_plots_days_into_hospitalisation.R
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#!/usr/bin/Rscript
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getwd()
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setwd('~/git/covid_analysis/')
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getwd()
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############################################################
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# TASK: Loess plots for days into hospital till T1
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############################################################
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#==========================================================
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#=============
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# input:source data
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#=============
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source("read_data.R")
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# clear unwanted variables
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rm(my_data, wf_data, lf_data)
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#=============
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# Output
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#=============
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output_plots_loess_hosp = paste0(outdir_plots, "output_plots_v3_loess_hosp.pdf")
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#%%========================================================
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#=====================
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# data for plots
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#=====================
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# remove PF
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table(lf_data_loess$mediator)
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lf_loess = lf_data_loess[lf_data_loess$mediator!= "PF",]
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table(lf_loess$mediator)
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#%=======================================================
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hosp_days_min = min(lf_loess$days_from_hospitalization_t1); hosp_days_min
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hosp_days_max = max(lf_loess$days_from_hospitalization_t1);hosp_days_max
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my_xscale_hosp = seq(hosp_days_min , hosp_days_max, 5)
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my_xscale_hosp
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#####################################################################
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# 95% CI: t1_data
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# days_from_hospitalization_t1
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#####################################################################
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lf_loess_t1 = lf_loess[lf_loess$timepoint == "t1",]
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# Output plots as one pdf
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cat("Output plots will be in:", output_plots_loess_hosp)
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pdf(output_plots_loess_hosp, width = 15, height = 8)
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#-----------
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# linear
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#-----------
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p1_hosp = ggplot(lf_loess_t1, aes(x = days_from_hospitalization_t1
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, y = value
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, colour = factor(outcomes))) +
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#geom_point() +
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geom_smooth(method = "loess", size = 1.5, na.rm = T) +
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facet_wrap(~mediator, nrow = 2, scales = "free_y")+
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labs(title = "Hospital days into t1: Linear scale and 95% CI"
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, x = "Days from hospitalisation to t1"
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, y = "T1 Levels")+
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scale_x_continuous(breaks = my_xscale_hosp, limits = c(hosp_days_min , hosp_days_max))+
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scale_colour_discrete(name = "Patient outcome"
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, labels = c("Death", "Recovered"))+
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theme(axis.text.x = element_text(size = 13)
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, axis.text.y = element_text(size = 13
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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 = 13)
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, axis.title.y = element_text(size = 13)
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, plot.title = element_text(size = 15, hjust = 0.5)
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, strip.text.x = element_text(size = 13, colour = "black")
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, legend.title = element_text(color = "black", size = 13)
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, legend.text = element_text(size = 13)
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, legend.position = "right"
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, legend.direction = "vertical")
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p1_hosp
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#-----------
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# log
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#-----------
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p2_hosp = ggplot(lf_loess_t1, aes(x = days_from_hospitalization_t1
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, y = value
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, colour = factor(outcomes))) +
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scale_y_log10()+
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#geom_point() +
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geom_smooth(method = "loess", size = 1.5, na.rm = T) +
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facet_wrap(~mediator, nrow = 2, scales = "free_y")+
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labs(title = "Hospital days into t1: Log scale and 95% CI"
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, x = "Days from hospitalisation to t1"
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, y = "T1 Levels (Log10)")+
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scale_x_continuous(breaks = my_xscale_hosp, limits = c(hosp_days_min , hosp_days_max))+
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scale_colour_discrete(name = "Patient outcome"
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, labels = c("Death", "Recovered"))+
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theme(axis.text.x = element_text(size = 13)
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, axis.text.y = element_text(size = 13
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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 = 13)
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, axis.title.y = element_text(size = 13)
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, plot.title = element_text(size = 15, hjust = 0.5)
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, strip.text.x = element_text(size = 13, colour = "black")
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, legend.title = element_text(color = "black", size = 13)
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, legend.text = element_text(size = 13)
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, legend.position = "right"
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, legend.direction = "vertical")
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p2_hosp
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#####################################################################
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# 50% CI: t1_data
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# days_from_hospitalization_t1
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#####################################################################
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#-----------
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# linear
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#-----------
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p3_hosp = ggplot(lf_loess_t1, aes(x = days_from_hospitalization_t1
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, y = value
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, colour = factor(outcomes))) +
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#geom_point() +
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geom_smooth(method = "loess", size = 1.5, na.rm = T, level = 0.50) +
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facet_wrap(~mediator, nrow = 2, scales = "free_y")+
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labs(title = "Hospital days into t1: Linear scale and 50% CI"
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, x = "Days from hospitalisation to t1"
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, y = "T1 Levels") +
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scale_x_continuous(breaks = my_xscale_hosp, limits = c(hosp_days_min , hosp_days_max))+
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scale_colour_discrete(name = "Patient outcome"
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, labels = c("Death", "Recovered"))+
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theme(axis.text.x = element_text(size = 13)
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, axis.text.y = element_text(size = 13
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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 = 13)
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, axis.title.y = element_text(size = 13)
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, plot.title = element_text(size = 15, hjust = 0.5)
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, strip.text.x = element_text(size = 13, colour = "black")
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, legend.title = element_text(color = "black", size = 13)
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, legend.text = element_text(size = 13)
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, legend.position = "right"
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, legend.direction = "vertical")
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p3_hosp
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#-----------
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# log
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#-----------
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p4_hosp = ggplot(lf_loess_t1, aes(x = days_from_hospitalization_t1
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, y = value
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, colour = factor(outcomes))) +
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scale_y_log10()+
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#geom_point() +
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geom_smooth(method = "loess", size = 1.5, na.rm = T, level = 0.50) +
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facet_wrap(~mediator, nrow = 2, scales = "free_y")+
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labs(title = "Hospital days into t1: Log scale and 50% CI"
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, x = "Days from hospitalisation to t1"
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, y = "T1 Levels (Log10)")+
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scale_x_continuous(breaks = my_xscale_hosp, limits = c(hosp_days_min , hosp_days_max))+
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scale_colour_discrete(name = "Patient outcome"
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, labels = c("Death", "Recovered"))+
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theme(axis.text.x = element_text(size = 13)
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, axis.text.y = element_text(size = 13
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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 = 13)
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, axis.title.y = element_text(size = 13)
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, plot.title = element_text(size = 15, hjust = 0.5)
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, strip.text.x = element_text(size = 13, colour = "black")
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, legend.title = element_text(color = "black", size = 13)
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, legend.text = element_text(size = 13)
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, legend.position = "right"
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, legend.direction = "vertical")
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p4_hosp
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dev.off()
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#####################################################################
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# 95% CI: Combined data *** only if required
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# days_from_hospitalization_t1
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#####################################################################
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#-----------
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# linear
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#-----------
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#p1_all_hosp = ggplot(lf_loess, aes(x = days_from_hospitalization_t1
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# , y = value
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# , colour = factor(outcomes))) +
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# #geom_point() +
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# geom_smooth(method = "loess", size = 1.5, na.rm = T, level = 0.90) +
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# facet_wrap(~mediator, nrow = 2, scales = "free_y")+
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# labs(title = "Hospital days into t1: linear scale and 95% CI"
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# , x = "Days from hospitalisation to t1"
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# , y = "Combined Levels")+
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# scale_x_continuous(breaks = my_xscale_hosp, limits = c(hosp_days_min , hosp_days_max))+
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# scale_colour_discrete(name = "Patient outcome"
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# , labels = c("Death", "Recovered"))
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#p1_all_hosp
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#-----------
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# log
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#-----------
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#p2_all_hosp = ggplot(lf_loess, aes(x = days_from_hospitalization_t1
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# , y = value
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# , colour = factor(outcomes))) +
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# scale_y_log10()+
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# #geom_point() +
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# geom_smooth(method = "loess", size = 1.5, na.rm = T) +
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# facet_wrap(~mediator, nrow = 2, scales = "free_y")+
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# labs(title = "Hospital days into t1: Log scale and 95% CI"
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# , x = "Days from hospitalisation to t1"
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# , y = "Combined Levels (Log10)")+
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# scale_x_continuous(breaks = my_xscale_hosp, limits = c(hosp_days_min , hosp_days_max))+
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# scale_colour_discrete(name = "Patient outcome"
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# , labels = c("Death", "Recovered"))
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#p2_all_hosp
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