plot_sample_corr_heatmap {proBatch} | R Documentation |
Plot correlation of selected samples
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), ...)
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
|
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
or pheatmap
object depending on flavor
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)