plot_PVCA.df: plot PVCA, when the analysis is completed

In symbioticMe/proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

plot PVCA, when the analysis is completed

Description

plot PVCA, when the analysis is completed

Usage

plot_PVCA.df(pvca_res, colors_for_bars = NULL, filename = NULL,
  width = NA, height = NA, units = c("cm", "in", "mm"),
  plot_title = NULL, theme = "classic", base_size = 20)

Arguments

pvca_res	data frame of weights of Principal Variance Components, result of calculate_PVCA
colors_for_bars	four-item color vector, specifying colors for the following categories: c('residual', 'biological', 'biol:techn', 'technical')
filename	path where the results are saved. If null the object is returned to the active window; otherwise, the object is save into the file. Currently only pdf and png format is supported
width	option determining the output image width
height	option determining the output image width
units	units: 'cm', 'in' or 'mm'
plot_title	title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc))
theme	ggplot theme, by default classic. Can be easily overriden

Value

ggplot object with bars as weights, colored by bio/tech factors

Examples

matrix_test <- example_proteome_matrix[1:150, ]
pvca_df_res <- prepare_PVCA_df(matrix_test, example_sample_annotation, 
technical_factors = c('MS_batch', 'digestion_batch'),
biological_factors = c("Diet", "Sex", "Strain"), 
pca_threshold = .6, variance_threshold = .01, fill_the_missing = -1)
colors_for_bars = c('grey', 'green','blue','red')
names(colors_for_bars) = c('residual', 'biological','biol:techn','technical')

pvca_plot <- plot_PVCA.df(pvca_df_res, colors_for_bars)

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.