plot_corr_matrix {proBatch}R Documentation

Visualise correlation matrix

Description

Plot correlation of selected samples or peptides

Usage

plot_corr_matrix(corr_matrix, flavor = c("pheatmap", "corrplot"),
  filename = NULL, width = NA, height = NA, unit = c("cm", "in",
  "mm"), plot_title = NULL, ...)

Arguments

corr_matrix

square correlation matrix

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

peptides <- c("10231_QDVDVWLWQQEGSSK_2", "10768_RLESELDGLR_2")

data_matrix_sub = example_proteome_matrix[peptides,]
corr_matrix = cor(t(data_matrix_sub), use = 'complete.obs')
corr_matrix_plot <- plot_corr_matrix(corr_matrix,  flavor = "corrplot")

[Package proBatch version 1.0.0 Index]