plot_heatmap {proBatch}R Documentation

Plot the heatmap of samples

Description

Plot the heatmap of samples

Usage

plot_heatmap(data_matrix, sample_annotation = NULL,
  sample_id_col = "FullRunName", sample_annotation_col = NULL,
  sample_annotation_row = NULL, fill_the_missing = TRUE,
  cluster_rows = TRUE, cluster_cols = FALSE,
  annotation_color_list = NA,
  heatmap_color = colorRampPalette(rev(RColorBrewer::brewer.pal(n = 7,
  name = "RdYlBu")))(100), color_for_missing = "black", filename = NA,
  plot_title = NA, ...)

Arguments

data_matrix

features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. in most function, it is assumed that this is the log transformed version of the original data

sample_annotation

data matrix with

  1. sample_id_col (this can be repeated as row names)

  2. biological and

  3. technical covariates (batches etc)

; each column of sample annotation will get it's own row. If cluster_cols = T this will indicate, whether sample proximity is driven by one of biolical or technical factors

sample_id_col

name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found)

sample_annotation_col

biological or technical factors to be annotated in heatmap columns

sample_annotation_row

biological or technical factors to be annotated in heatmap rows

fill_the_missing

boolean value determining if missing values should be substituted with -1 (and colored with black)

cluster_rows

boolean value determining if rows should be clustered

cluster_cols

boolean value determining if columns should be clustered

annotation_color_list

list specifying colors for columns (samples). Best created by sample_annotation_to_colors

heatmap_color

vector of colors used in heatmap (typicall a gradient)

color_for_missing

special color to make missing values. Usually black or white, depending on heatmap_color

filename

filepath where to save the image

plot_title

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

...

other parameters of link[pheatmap]{pheatmap}

Value

object returned by link[pheatmap]{pheatmap}

See Also

sample_annotation_to_colors, pheatmap

Examples

color_scheme <- sample_annotation_to_colors (example_sample_annotation, 
factor_columns = c('MS_batch','EarTag', "Strain", 
"Diet", "digestion_batch", "Sex"),
not_factor_columns = 'DateTime',
numeric_columns = c('order'))

heatmap_plot <- plot_heatmap(example_proteome_matrix, 
example_sample_annotation, 
sample_annotation_col = c("MS_batch",  "digestion_batch", "Diet"), 
cluster_cols = TRUE, 
annotation_color_list = color_scheme$list_of_colors,
show_rownames = FALSE, show_colnames = FALSE)


[Package proBatch version 1.0.0 Index]