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isolating function from running on data

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This commit is contained in:
Tanushree Tunstall 2020-11-01 16:44:42 +00:00
parent eaa8416255
commit c0d993b232
1 changed files with 1 additions and 51 deletions
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52
boxplot_stat_function.R
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@ -26,7 +26,6 @@ doMyPlots <- function(df) {
#, palette = c("#00BFC4", "#F8766D") #, palette = c("#00BFC4", "#F8766D")
))+ ))+
scale_colour_manual(values=c("#00BFC4", "#F8766D")) + scale_colour_manual(values=c("#00BFC4", "#F8766D")) +
scale_y_log10()
theme(axis.text.x = element_text(size = 15) theme(axis.text.x = element_text(size = 15)
, axis.text.y = element_text(size = 15 , axis.text.y = element_text(size = 15
, angle = 0 , angle = 0
@ -50,7 +49,6 @@ doMyPlots <- function(df) {
stat_df <- stat_df %>% stat_df <- stat_df %>%
add_xy_position(x = "timepoint", dodge = 0.8) add_xy_position(x = "timepoint", dodge = 0.8)
cat("printing p")
p2 = p + stat_pvalue_manual(stat_df p2 = p + stat_pvalue_manual(stat_df
#, y.position = max_y #, y.position = max_y
, label = "{p_format} {p.signif}" , label = "{p_format} {p.signif}"
@ -63,52 +61,4 @@ doMyPlots <- function(df) {
return(plots) return(plots)
} }
############################################################### ###############################################################
#============
# test
#============
source("boxplot_linear.R")
#=============
# Output:
#=============
outfile_bp = paste0("boxplots_TEST", ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
#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,]
foo=doMyPlots(lf_test)
#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
baz
#dev.off()
##################################################################
#=========================
# entire sample_type data
#=========================
my_sample_type = "NPA"
outfile_bp = paste0("boxplots_stats_", my_sample_type, ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16)
#===========================
# combine: ggpubr::ggarrange
#===========================
plots_npa = doMyPlots(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_type, color = "purple", face = "bold", size = 14)
, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
, color = "blue"
, hjust = 1, x = 0.98, face = "italic", size = 10)
, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18)
#, right = "I'm done, thanks :-)!",
#, fig.lab = "Figure 1", fig.lab.face = "bold"
)
npa_plot_annot
dev.off()