plot_PCA: plot PCA plot

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

plot PCA plot

Description

plot PCA plot

Usage

plot_PCA(data_matrix, sample_annotation,
  feature_id_col = "peptide_group_label",
  sample_id_col = "FullRunName", color_by = "MS_batch",
  PC_to_plot = c(1, 2), fill_the_missing = -1,
  color_scheme = "brewer", filename = NULL, width = NA,
  height = NA, units = c("cm", "in", "mm"), plot_title = NULL,
  theme = "classic", base_size = 20)

Arguments

data_matrix	features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. See "example_proteome_matrix" for more details (to call the description, use help("example_proteome_matrix"))
sample_annotation	data frame with: sample_id_col (this can be repeated as row names) biological covariates technical covariates (batches etc) . See help("example_sample_annotation")
feature_id_col	name of the column with feature/gene/peptide/protein ID used in the long format representation df_long. In the wide formatted representation data_matrix this corresponds to the row names.
sample_id_col	name of the column in sample_annotation table, where the filenames (colnames of the data_matrix are found).
color_by	column name (as in sample_annotation) to color by
PC_to_plot	principal component numbers for x and y axis
fill_the_missing	numeric value determining how missing values should be substituted. If NULL, features with missing values are excluded. If NULL, features with missing values are excluded.
color_scheme	a named vector of colors to map to batch_col, names corresponding to the levels of the factor. For continuous variables, vector doesn't need to be named.
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 scatterplot colored by factor levels of column specified in factor_to_color

See Also

autoplot.pca_common, ggplot

Examples

pca_plot <- plot_PCA(example_proteome_matrix, example_sample_annotation, 
color_by = 'MS_batch', plot_title = "PCA colored by MS batch")
pca_plot <- plot_PCA(example_proteome_matrix, example_sample_annotation, 
color_by = 'DateTime', plot_title = "PCA colored by DateTime")

color_list <- sample_annotation_to_colors (example_sample_annotation, 
factor_columns = c('MS_batch', 'digestion_batch'),
numeric_columns = c('DateTime','order'))
pca_plot <- plot_PCA(example_proteome_matrix, example_sample_annotation, 
color_by = 'DateTime', color_scheme = color_list[['DateTime']])

## Not run: 
pca_plot <- plot_PCA(example_proteome_matrix, example_sample_annotation, 
color_by = 'DateTime', plot_title = "PCA colored by DateTime",
filename = 'test_PCA.png', width = 14, height = 9, units = 'cm')

## End(Not run)

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