plot_sample_corr_distribution {proBatch}R Documentation

Create violin plot of correlation distribution

Description

Useful to visualize within batch vs within replicate vs non-related sample correlation

Usage

plot_sample_corr_distribution(data_matrix, sample_annotation,
  repeated_samples = NULL, sample_id_col = "FullRunName",
  batch_col = "MS_batch", biospecimen_id_col = "EarTag",
  plot_title = "Correlation distribution",
  plot_param = "batch_replicate")

Arguments

data_matrix

features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. Usually the log transformed version of the original data

sample_annotation

data matrix with 1) sample_id_col (this can be repeated as row names) 2) biological and 3) technical covariates (batches etc)

repeated_samples

if NULL, only repeated sample correlation is plotted

sample_id_col

name of the column in sample_annotation file, where the filenames (colnames of the data matrix) are found

batch_col

column in sample_annotation that should be used for batch comparison

biospecimen_id_col

column in sample_annotation that captures the biological sample, that (possibly) was profiled several times as technical replicates. Tip: if such ID is absent, but can be defined from several columns, create new biospecimen_id column

plot_title

Title of the plot (usually, processing step + representation level (fragments, transitions, proteins))

plot_param

columns, defined in correlation_df, which is output of get_sample_corr_distrib, specifically, #'

  1. replicate

  2. batch_the_same

  3. batch_replicate

  4. batches

;

Value

ggplot type object with violin plot for each plot_param

See Also

get_sample_corr_distrib, ggplot

Examples

sample_corr_distribution_plot <- plot_sample_corr_distribution(
example_proteome_matrix,
example_sample_annotation, batch_col = 'MS_batch', 
biospecimen_id_col = "EarTag", 
plot_param = 'batch_replicate')


[Package proBatch version 1.0.0 Index]