plot_PCA: plot PCA plot

View source: R/proteome_wide_diagnostics.R

plot_PCAR Documentation

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:

  1. sample_id_col (this can be repeated as row names)

  2. biological covariates

  3. 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.