added boxplots_stat_ob_paper.R and plot_data_ob_paper.R
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plot_data_ob_paper.R
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plot_data_ob_paper.R
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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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# Graphs for paper?
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#============
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# Mediators required
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#============
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#NPA and Serum
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#IFNa2a
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#IFN-b
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#IFN-g
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#IL-1
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#IL-6
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#IL-8
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#IP-10
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#TNF-a
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#vl_pfu_ul
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#Figure 1a: Study design
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#Figure 1b: Viral load
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#Figure 1c: NPA
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#Figure 1d: Serum
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############################################################
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#=============
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# Input
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#=============
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source("data_extraction_mediators.R")
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# check: adult variable and age variable discrepancy!
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metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
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#===============================
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# data assignment for plots
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#================================
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#time_letter = "t"
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time_letter = "T"
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#-----------
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# npa
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#-----------
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wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
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lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
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lf_fp_npa$timepoint = paste0(time_letter, 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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head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
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lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
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table(lf_fp_npa$mediator)
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table(lf_fp_npa$sample_type, lf_fp_npa$timepoint)
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a = lf_fp_npa %>%
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select(matches("^(vl_pfu|timepoint|mediator|sample_type)"))
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table(a$sample_type)
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#-----------
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# serum
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#-----------
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wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
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lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
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lf_fp_serum$timepoint = paste0(time_letter, 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$obesity)
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head(lf_fp_serum$value[lf_fp_serum$mediator == "vitd"])
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########################################################################
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rm(npa_lf, sam_lf, serum_lf)
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########################################################################
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viral_load_npa = c("vl_pfu_ul")
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selected_mediators = c("ifna2a", "ifnb", "ifn", "il1", "il6", "il8", "ip10", "tnf")
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cols_to_select = c("mosaic", "obesity", "flustat", "asthma",
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"sample_type", "timepoint", "mediator", "value" )
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# sanity checks
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table(lf_fp_npa$mediator, lf_fp_npa$timepoint)
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class(lf_fp_npa$mediator)
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str(lf_fp_npa)
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table(lf_fp_npa$mediator)
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# selected dfs for plotting for paper
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#--------
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# VL: NPA
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#--------
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vl_lf_plot = lf_fp_npa[lf_fp_npa$mediator%in%viral_load_npa,]
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vl_lf_plot_df = vl_lf_plot[,colnames(vl_lf_plot)%in%cols_to_select]
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a6 = vl_lf_plot_df
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table(vl_lf_plot $mediator, vl_lf_plot$timepoint, vl_lf_plot$sample_type)
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table(vl_lf_plot$sample_type)
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table(lf_fp_npa$sample_type)
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a5 = npa_wf%>%
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select(matches("^(vl_pfu|mosaic)"))
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identical(a5$vl_pfu_ul_npa1, a5$vl_pfu_ul_npa1.1)
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# Minor fix: somehow upstream introduced this...
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table(vl_lf_plot_df$sample_type[vl_lf_plot_df$sample_type == "npa1."])
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table(vl_lf_plot_df$sample_type[vl_lf_plot_df$sample_type == "npa"])
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vl_lf_plot_df$sample_type[vl_lf_plot_df$sample_type == "npa1."] <- "npa"
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table(vl_lf_plot_df$sample_type[vl_lf_plot_df$sample_type == "npa1."])
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table(vl_lf_plot_df$sample_type)
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#==========================
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# DFs for plotting: VL NPA
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#==========================
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# linear: raw values
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dim(vl_lf_plot_df)
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table(vl_lf_plot_df$mediator, vl_lf_plot_df$timepoint)
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table(vl_lf_plot_df$sample_type, vl_lf_plot_df$timepoint)
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# display names
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vl_lf_plot_df$mediator[vl_lf_plot_df$mediator == "vl_pfu_ul"] <- "Viral load" # U+03B1
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# log values: log10
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vl_lf_plot_df_log = vl_lf_plot_df
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table(vl_lf_plot_df_log$mediator=="Viral load")
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# vl data juggling with 0!
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vl_lf_plot_df_log$value[1:30]
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table(vl_lf_plot_df_log$value == 0)
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vl_lf_plot_df_log$value[vl_lf_plot_df_log$value == 0] <- 1
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vl_lf_plot_df_log$value[1:30]
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table(vl_lf_plot_df_log$value == 1)
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orig_nrow = nrow(vl_lf_plot_df_log); orig_nrow; table(vl_lf_plot_df_log$mediator)
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head(vl_lf_plot_df_log$value)
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# log all values and reassign
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vl_lf_plot_df_log$value = log10(vl_lf_plot_df_log$value)
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vl_lf_plot_df_log$value[1:30]
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##############################################################
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#--------
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# NPA: mediators
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#--------
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# linear: raw values
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npa_lf_plot = lf_fp_npa[lf_fp_npa$mediator%in%selected_mediators,]
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npa_lf_plot_df = npa_lf_plot[,colnames(npa_lf_plot)%in%cols_to_select]
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table(npa_lf_plot_df$sample_type)
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table(npa_lf_plot_df$sample_type,npa_lf_plot_df$timepoint, npa_lf_plot_df$mediator )
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# Display names
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "ifna2a"] <- "IFN-α2a" # U+03B1
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "ifnb"] <- "IFN-β" # U+03B2
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "ifn"] <- "IFN-γ" # U+03B3
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "il1"] <- "IL-1"
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "il6"] <- "IL-6"
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "il8"] <- "CXCL8"
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "ip10"] <- "CXCL10"
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npa_lf_plot_df$mediator[npa_lf_plot_df$mediator == "tnf"] <- "TNF-α" # U+03B1
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# check display names
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table(npa_lf_plot_df$mediator)
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# log values: log10
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npa_lf_plot_df_log = npa_lf_plot_df
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table(npa_lf_plot_df_log$value == 1.000000e+04)
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table(npa_lf_plot_df_log$value == 0)
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# log all values and reassign
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npa_lf_plot_df_log$value[1:10]
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npa_lf_plot_df_log$value = log10(npa_lf_plot_df_log$value)
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npa_lf_plot_df_log$value[1:10]
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# check display names
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table(npa_lf_plot_df_log$mediator)
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#--------
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# Serum: mediators
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#--------
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# linear: raw values
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serum_lf_plot = lf_fp_serum[lf_fp_serum$mediator%in%selected_mediators,]
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serum_lf_plot_df = serum_lf_plot[,colnames(serum_lf_plot)%in%cols_to_select]
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table(serum_lf_plot_df$sample_type)
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table(serum_lf_plot_df$sample_type,serum_lf_plot_df$timepoint, serum_lf_plot_df$mediator )
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# Display names: Serum
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "ifna2a"] <- "IFN-α2a" # U+03B1
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "ifnb"] <- "IFN-β" # U+03B2
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "ifn"] <- "IFN-γ" # U+03B3
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "il1"] <- "IL-1"
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "il6"] <- "IL-6"
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "il8"] <- "CXCL8"
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "ip10"] <- "CXCL10"
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serum_lf_plot_df$mediator[serum_lf_plot_df$mediator == "tnf"] <- "TNF-α" # U+03B1
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# check display names
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table(serum_lf_plot_df$mediator)
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# log values: log10
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serum_lf_plot_log = serum_lf_plot_df
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table(serum_lf_plot_log$value == 1.000000e+04)
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table(serum_lf_plot_log$value == 0)
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# log all values and reassign
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serum_lf_plot_log$value[1:10]
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serum_lf_plot_log$value = log10(serum_lf_plot$value)
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serum_lf_plot_log$value[1:10]
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# check display names
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table(serum_lf_plot_log$mediator)
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########################################################################
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# remove variables
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rm(vl_lf_plot, npa_lf_plot, serum_lf_plot)
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