In MassDynamics/lfq_processing: Processes Proteomics Files for Quantification.

knitr::opts_chunk$set(fig.cap = NULL, fig.path = params$output_figure,  dev = "svg")

library(knitr)
library(data.table)
library(ggplot2)
library(ggrepel)
library(GGally)
library(umap)
library(FactoMineR)
library(factoextra)
library(corrplot)
library(viridis)
library(ggpubr)
library(Hmisc)
library(plotly)
library(stringr)
library(bit64)

evidence <- generic_mq_table_reader(upload_folder, 'evidence.txt')

evidence$`raw file` <- as.character(evidence$`raw file`)
p <- ggplot(evidence, aes(x = `raw file`, y = pif, fill = '#AEC6CF', colour = '#AEC6CF')) +
  geom_boxplot() +
  #geom_violin() +
  theme_minimal() +
  #coord_cartesian(ylim = c(0, boxplot.stats(fdt[, fwhm])$stats[ 5])) +
   theme(axis.text.x = element_text(angle = 90, vjust = 0.2),
        panel.grid.major.y = element_blank(),
        panel.border = element_blank(),
        axis.ticks.y = element_blank(),
        legend.position = "none"
  ) +
  scale_x_discrete("Raw File") +
  scale_y_continuous("Precursor Ion Fraction") +
  ggtitle("Parent ion fraction")
p