added boxplot_stat_log.R to generate graphs with log data and stats
This commit is contained in:
parent
550e8b2c50
commit
b8ff7995ac
6 changed files with 249 additions and 10 deletions
|
|
@ -28,7 +28,7 @@ fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
|
|||
cat("\nPlotting boxplots with stats for:", my_sample_npa
|
||||
, "\n========================================================\n")
|
||||
|
||||
plots_npa = doMyPlots(lf_fp_npa)
|
||||
plots_npa = doMyPlotsStats(lf_fp_npa)
|
||||
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
|
||||
, align = "hv"
|
||||
, ncol = 7
|
||||
|
|
@ -94,7 +94,7 @@ fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
|
|||
cat("\nPlotting boxplots with stats for:", my_sample_serum
|
||||
, "\n========================================================\n")
|
||||
|
||||
plots_serum = doMyPlots(lf_fp_serum)
|
||||
plots_serum = doMyPlotsStats(lf_fp_serum)
|
||||
serum_plot = ggpubr::ggarrange(plotlist = plots_serum
|
||||
, align = "hv"
|
||||
, ncol = 7
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ getwd()
|
|||
############################################################
|
||||
# TASK: boxplots with stats
|
||||
############################################################
|
||||
doMyPlots <- function(df) {
|
||||
doMyPlotsStats <- function(df) {
|
||||
mediators = levels(as.factor(df$mediator))
|
||||
|
||||
plots <- list()
|
||||
|
|
@ -62,3 +62,4 @@ doMyPlots <- function(df) {
|
|||
}
|
||||
|
||||
###############################################################
|
||||
|
||||
|
|
|
|||
|
|
@ -22,8 +22,16 @@ pdf(output_boxplot_stats, width=22, height=16)
|
|||
#med_names = c("eotaxin3", "il12p70", "itac", "il13")
|
||||
#lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
|
||||
|
||||
#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
|
||||
foo_annot = annotate_figure(foo
|
||||
baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
|
||||
baz
|
||||
|
||||
sam_plot = ggpubr::ggarrange(plotlist = foo
|
||||
, align = "hv"
|
||||
, ncol = 7
|
||||
, nrow = 5
|
||||
, common.legend = T)
|
||||
sam_plot
|
||||
foo_annot = annotate_figure(sam_plot
|
||||
, top = text_grob(my_sample_name
|
||||
, color = "blue"
|
||||
, face = "bold"
|
||||
|
|
@ -41,3 +49,80 @@ foo_annot = annotate_figure(foo
|
|||
foo_annot
|
||||
dev.off()
|
||||
##################################################################
|
||||
# ind components of function
|
||||
my_sample_name = "SAM"
|
||||
to_remove = c("ifna2a"
|
||||
, "il29")
|
||||
|
||||
lf_fp_sam2 = lf_fp_sam[!lf_fp_sam$mediator%in%to_remove,]
|
||||
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
|
||||
|
||||
df_test = lf_fp_sam3
|
||||
df_test = lf_fp_sam2
|
||||
table(df_test$mediator)
|
||||
|
||||
p = ggplot(df_test)+ geom_boxplot(aes(x = timepoint
|
||||
, y = value
|
||||
, color = obesity
|
||||
#, palette = c("#00BFC4", "#F8766D")
|
||||
))+
|
||||
scale_colour_manual(values=c("#00BFC4", "#F8766D")) +
|
||||
theme(axis.text.x = element_text(size = 15)
|
||||
, axis.text.y = element_text(size = 15
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_blank()
|
||||
, axis.title.y = element_blank()
|
||||
, legend.position = "none"
|
||||
, plot.subtitle = element_text(size = 20, hjust = 0.5)
|
||||
, plot.title = element_text(size = 20, hjust = 0.5)) +
|
||||
labs(title = "TEST")
|
||||
p
|
||||
|
||||
#--------
|
||||
# stats
|
||||
#---------
|
||||
to_remove = c("ifna2a"
|
||||
, "il29")
|
||||
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
|
||||
|
||||
lf_fp_sam4 = lf_fp_sam3[lf_fp_sam3$timepoint == "t3",]
|
||||
table(lf_fp_sam4$timepoint)
|
||||
|
||||
wilcox_test(value~obesity, data = lf_fp_sam4)
|
||||
|
||||
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
|
||||
time = c("t3")
|
||||
lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$timepoint%in%time,]
|
||||
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
|
||||
|
||||
med = c("il29")
|
||||
time2 = c("t2")
|
||||
|
||||
lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$mediator%in%med && lf_fp_sam3$timepoint%in%time2,]
|
||||
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
|
||||
|
||||
df_test = lf_fp_sam3
|
||||
|
||||
|
||||
table(df_test$mediator)
|
||||
|
||||
|
||||
stat_df <- df_test %>%
|
||||
group_by(timepoint, mediator) %>%
|
||||
wilcox_test(value ~ obesity, paired = F) %>%
|
||||
add_significance("p")
|
||||
stat_df$p_format = round(stat_df$p, digits = 3)
|
||||
|
||||
|
||||
stat_df <- stat_df %>%
|
||||
add_xy_position(x = "timepoint", dodge = 0.8)
|
||||
p2 = p + stat_pvalue_manual(stat_df
|
||||
#, y.position = max_y
|
||||
, label = "{p_format} {p.signif}"
|
||||
, hide.ns = T
|
||||
, tip.length = 0)+
|
||||
scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
|
||||
|
||||
p2
|
||||
|
|
|
|||
153
boxplot_stat_log.R
Normal file
153
boxplot_stat_log.R
Normal file
|
|
@ -0,0 +1,153 @@
|
|||
#!/usr/bin/Rscript
|
||||
getwd()
|
||||
setwd("~/git/mosaic_2020/")
|
||||
getwd()
|
||||
###############################################################
|
||||
#=============
|
||||
# Input
|
||||
#=============
|
||||
source("boxplot_stat_function.R")
|
||||
source("plot_data.R")
|
||||
|
||||
#=============
|
||||
# Output
|
||||
#=============
|
||||
outfile_bp = paste0("boxplots_stats_npa_serum_LOG", ".pdf")
|
||||
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
|
||||
pdf(output_boxplot_stats, width=22, height=16)
|
||||
###############################################################
|
||||
#===============================
|
||||
# data assignment for plots
|
||||
#===============================
|
||||
#----------------------------------------
|
||||
#-------
|
||||
# NPA
|
||||
#-------
|
||||
# vl data juggling with 0!
|
||||
vl_temp_fix = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
|
||||
vl_temp_fix$value[1:20]
|
||||
vl_temp_fix$value[vl_temp_fix$value == 0] <- 1
|
||||
vl_temp_fix$value[1:20]
|
||||
|
||||
orig_nrow = nrow(lf_fp_npa); orig_nrow; table(lf_fp_npa$mediator)
|
||||
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator=="vl_pfu_ul",]
|
||||
temp_nrow = nrow(lf_fp_npa); temp_nrow; table(lf_fp_npa$mediator)
|
||||
|
||||
# add vl_temp_fix back
|
||||
lf_fp_npa = rbind(lf_fp_npa, vl_temp_fix)
|
||||
revised_nrow = nrow(lf_fp_npa); revised_nrow
|
||||
|
||||
orig_nrow == revised_nrow
|
||||
|
||||
head(lf_fp_npa$value)
|
||||
|
||||
# log all values and reassign
|
||||
lf_fp_npa$value = log10(lf_fp_npa$value)
|
||||
head(lf_fp_npa$value)
|
||||
vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
|
||||
vl_temp_fix2$value[1:20]
|
||||
|
||||
#------------------------------------------
|
||||
my_sample_npa = "NPA"
|
||||
fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
|
||||
|
||||
cat("\nPlotting boxplots with stats for:", my_sample_npa
|
||||
, "\n========================================================\n")
|
||||
|
||||
plots_npa = doMyPlotsStats(lf_fp_npa)
|
||||
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
|
||||
, align = "hv"
|
||||
, ncol = 7
|
||||
, nrow = 5
|
||||
, common.legend = T)
|
||||
#npa_plot
|
||||
npa_plot_annot = annotate_figure(npa_plot
|
||||
, top = text_grob(my_sample_npa
|
||||
, color = "blue"
|
||||
, face = "bold"
|
||||
, size = 14)
|
||||
, bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")")
|
||||
, color = "blue"
|
||||
, hjust = 1
|
||||
, x = 0.98
|
||||
, face = "italic"
|
||||
, size = 10)
|
||||
, left = text_grob("Levels (pg/ml)"
|
||||
, color = "black"
|
||||
, rot = 90
|
||||
, size = 18))
|
||||
npa_plot_annot
|
||||
#dev.off()
|
||||
#-------------
|
||||
# SAM
|
||||
#-------------
|
||||
#my_sample_sam = "SAM"
|
||||
#fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
|
||||
|
||||
#cat("\nPlotting boxplots with stats for:", my_sample_sam
|
||||
# , "\n========================================================\n")
|
||||
|
||||
#plots_sam = doMyPlots(lf_fp_sam)
|
||||
#sam_plot = ggpubr::ggarrange(plotlist = plots_sam
|
||||
# , align = "hv"
|
||||
# , ncol = 7
|
||||
# , nrow = 5
|
||||
# , common.legend = T)
|
||||
#sam_plot
|
||||
#sam_plot_annot = annotate_figure(sam_plot
|
||||
# , top = text_grob(my_sample_sam
|
||||
# , color = "blue"
|
||||
# , face = "bold"
|
||||
# , size = 14)
|
||||
# , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")")
|
||||
# , color = "blue"
|
||||
# , hjust = 1
|
||||
# , x = 0.98
|
||||
# , face = "italic"
|
||||
# , size = 10)
|
||||
# , left = text_grob("Levels (pg/ml)"
|
||||
# , color = "black"
|
||||
# , rot = 90
|
||||
# , size = 18))
|
||||
#sam_plot_annot
|
||||
#dev.off()
|
||||
#------------------------------------------
|
||||
#-------------
|
||||
# SERUM
|
||||
#-------------
|
||||
head(lf_fp_serum$value)
|
||||
# reassign
|
||||
lf_fp_serum$value = log10(lf_fp_serum$value)
|
||||
head(lf_fp_serum$value)
|
||||
|
||||
my_sample_serum = "serum"
|
||||
fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
|
||||
|
||||
cat("\nPlotting boxplots with stats for:", my_sample_serum
|
||||
, "\n========================================================\n")
|
||||
|
||||
plots_serum = doMyPlotsStats(lf_fp_serum)
|
||||
serum_plot = ggpubr::ggarrange(plotlist = plots_serum
|
||||
, align = "hv"
|
||||
, ncol = 7
|
||||
, nrow = 5
|
||||
, common.legend = T)
|
||||
#serum_plot
|
||||
serum_plot_annot = annotate_figure(serum_plot
|
||||
, top = text_grob(my_sample_serum
|
||||
, color = "blue"
|
||||
, face = "bold"
|
||||
, size = 14)
|
||||
, bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")")
|
||||
, color = "blue"
|
||||
, hjust = 1
|
||||
, x = 0.98
|
||||
, face = "italic"
|
||||
, size = 10)
|
||||
, left = text_grob("Levels (pg/ml)"
|
||||
, color = "black"
|
||||
, rot = 90
|
||||
, size = 18))
|
||||
serum_plot_annot
|
||||
dev.off()
|
||||
###############################################################
|
||||
|
|
@ -9,7 +9,7 @@ getwd()
|
|||
#=============
|
||||
# Input
|
||||
#=============
|
||||
source("boxplot_linear.R")
|
||||
source("plot_data.R")
|
||||
#######################################################
|
||||
med_names = c("eotaxin3", "il12p70", "itac", "il13")
|
||||
lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@ metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
|
|||
#-----------
|
||||
# npa
|
||||
#-----------
|
||||
#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
|
||||
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)
|
||||
lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
|
||||
|
|
@ -35,7 +35,7 @@ table(lf_fp_npa$mediator)
|
|||
#-----------
|
||||
# sam
|
||||
#-----------
|
||||
#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
|
||||
wf_fp_sam = sam_wf[sam_wf$flustat == 1,]
|
||||
lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
|
||||
lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
|
||||
lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
|
||||
|
|
@ -49,7 +49,7 @@ table(lf_fp_sam$mediator)
|
|||
#-----------
|
||||
# serum
|
||||
#-----------
|
||||
#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
|
||||
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)
|
||||
lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue