plot_sample_corr_heatmap {proBatch} | R Documentation |
Plot correlation of selected samples
plot_sample_corr_heatmap( data_matrix, samples_to_plot = NULL, sample_annotation = NULL, sample_id_col = "FullRunName", factors_to_plot = NULL, cluster_rows = FALSE, cluster_cols = FALSE, heatmap_color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100), color_list = NULL, filename = NULL, width = NA, height = NA, units = c("cm", "in", "mm"), plot_title = sprintf("Correlation matrix of%s samples", ifelse(is.null(samples_to_plot), "", " selected")), ... )
data_matrix |
features (in rows) vs samples (in columns) matrix, with
feature IDs in rownames and file/sample names as colnames.
See "example_proteome_matrix" for more details (to call the description,
use |
samples_to_plot |
string vector of samples in
|
sample_annotation |
data frame with:
.
See |
sample_id_col |
name of the column in |
factors_to_plot |
vector of technical and biological covariates to be
plotted in this diagnostic plot (assumed to be present in
|
cluster_rows |
boolean values determining if rows should be clustered or |
cluster_cols |
boolean values determining if columns should be clustered or |
heatmap_color |
vector of colors used in heatmap. |
color_list |
list, as returned by |
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 |
units |
units: 'cm', 'in' or 'mm' |
plot_title |
title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc)) |
... |
parameters for the |
pheatmap
object
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, factors_to_plot = c('MS_batch','Diet', 'DateTime', 'digestion_batch'), cluster_rows= FALSE, cluster_cols=FALSE, annotation_names_col = TRUE, annotation_legend = FALSE, show_colnames = FALSE) color_list <- sample_annotation_to_colors (example_sample_annotation, factor_columns = c('MS_batch','EarTag', "Strain", "Diet", "digestion_batch", "Sex"), numeric_columns = c('DateTime', 'order')) sample_corr_heatmap_annotated <- plot_sample_corr_heatmap(log_transform_dm(example_proteome_matrix), sample_annotation = example_sample_annotation, factors_to_plot = c('MS_batch','Diet', 'DateTime', 'digestion_batch'), cluster_rows= FALSE, cluster_cols=FALSE, annotation_names_col = TRUE, show_colnames = FALSE, color_list = color_list)