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This commit is contained in:
Tanushree Tunstall 2020-10-30 13:22:47 +00:00
parent d512fd4e34
commit 7946d8cf72
1 changed files with 12 additions and 5 deletions
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17
boxplot_linear.R
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@ -24,6 +24,9 @@ output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
#===============================
# data assignment for plots
#================================
#-----------
# npa
#-----------
#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
@ -34,7 +37,9 @@ table(lf_fp_npa$mediator)
head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
#-----------
# sam
#-----------
#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
@ -45,7 +50,9 @@ table(lf_fp_sam$mediator)
head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
#-----------
# serum
#-----------
#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
@ -63,7 +70,7 @@ if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
cat ("PASS: required groups are factors")
}
#------------------------------------------
title_npa_linear = "Boxplot: NPA (Linear)"
title_npa_linear = "NPA (Linear)"
#-----------------------------------------
bxp_npa_linear <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
@ -96,7 +103,7 @@ if (is.factor(lf_fp_sam$timepoint) && is.factor(lf_fp_sam$timepoint)){
}
#------------------------------------------
title_sam_linear = "Boxplot: sam (Linear)"
title_sam_linear = "SAM (Linear)"
#-----------------------------------------
bxp_sam_linear <- ggboxplot(lf_fp_sam, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
@ -130,7 +137,7 @@ if (is.factor(lf_fp_serum$timepoint) && is.factor(lf_fp_serum$timepoint)){
table(lf_fp_serum$mediator)
#------------------------------------------
title_serum_linear = "Boxplot: serum (Linear)"
title_serum_linear = "SERUM (Linear)"
#-----------------------------------------
bxp_serum_linear <- ggboxplot(lf_fp_serum, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +