plot_protein_corrplot {proBatch} | R Documentation |
Plots correlation plot of peptides from a single protein
plot_protein_corrplot(data_matrix, protein_name, peptide_annotation, protein_col = "ProteinName", feature_id_col = "peptide_group_label", flavor = c("pheatmap", "corrplot"), filename = NULL, width = NA, height = NA, unit = c("cm", "in", "mm"), plot_title = sprintf("Peptide correlation matrix of %s protein", protein_name), ...)
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 |
protein_name |
the name of the protein |
peptide_annotation |
df with peptides and their corresponding proteins |
protein_col |
the column name in |
feature_id_col |
name of the column with feature/gene/peptide/protein
ID used in the long format representation |
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 |
The title of the plot |
... |
parameters for the corrplot visualisation |
corrplot
or pheatmap
object depending on flavor
protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, protein_name = 'Haao', peptide_annotation = example_peptide_annotation, protein_col = 'Gene', flavor = "pheatmap")