plot_sample_corr_heatmap {proBatch}R Documentation

Sample correlation matrix (heatmap)

Description

Plot correlation of selected samples

Usage

plot_sample_corr_heatmap(data_matrix, samples_to_plot = NULL,
  flavor = c("pheatmap", "corrplot"), filename = NULL, width = NA,
  height = NA, unit = c("cm", "in", "mm"),
  plot_title = sprintf("Correlation matrix of sample %s",
  samples_to_plot), ...)

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

samples_to_plot

string vector of samples in data_matrix to be used in the plot

flavor

either corrplot from 'corrplot' package or heatmap, as in 'pheatmap'

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

unit

units: 'cm', 'in' or 'mm'

plot_title

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

...

parameters for the corrplot.mixed or pheatmap visualisation, for details see examples and help to corresponding functions

Value

corrplot or pheatmap object depending on flavor

See Also

pheatmap, corrplot.mixed

Examples

specified_samples = example_sample_annotation$FullRunName[
which(example_sample_annotation$order %in% 110:115)] 

sample_corr_heatmap <- plot_sample_corr_heatmap(example_proteome_matrix, 
samples_to_plot = specified_samples, 
 flavor = 'pheatmap', 
 cluster_rows= FALSE, cluster_cols=FALSE,
 annotation_names_col = TRUE, annotation_legend = FALSE, 
 show_colnames = FALSE)


[Package proBatch version 1.0.0 Index]