plot_heatmap_generic: Plot the heatmap

Description Usage Arguments Value Examples

View source: R/proteome_wide_diagnostics.R

Description

Plot the heatmap

Usage

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plot_heatmap_generic(
  data_matrix,
  column_annotation_df = NULL,
  row_annotation_df = NULL,
  col_ann_id_col = "FullRunName",
  row_ann_id_col = "peptide_group_label",
  columns_for_cols = c("MS_batch", "Diet", "DateTime", "order"),
  columns_for_rows = c("KEGG_pathway", "WGCNA_module", "evolutionary_distance"),
  cluster_rows = FALSE,
  cluster_cols = TRUE,
  annotation_color_cols = NULL,
  annotation_color_rows = NULL,
  fill_the_missing = -1,
  color_for_missing = "black",
  heatmap_color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),
  filename = NULL,
  width = 7,
  height = 7,
  units = c("cm", "in", "mm"),
  plot_title = NULL,
  ...
)

Arguments

data_matrix

the matrix of data to be plotted

column_annotation_df

data frame annotating columns of data_matrix

row_annotation_df

data frame annotating rows of data_matrix

col_ann_id_col

column of column_annotation_df whose values are unique identifiers of columns in data_matrix

row_ann_id_col

column of row_annotation_df whose values are unique identifiers of rows in data_matrix

columns_for_cols

vector of factors (columns) of column_annotation_df that will be mapped to color annotation of heatmap columns

columns_for_rows

vector of factors (columns) of row_annotation_df that will be mapped to color annotation of heatmap rows

cluster_rows

boolean: whether the rows should be clustered

cluster_cols

boolean: whether the rows should be clustered

annotation_color_cols

list of color vectors for column annotation, for each factor to be plotted; for factor-like variables a named vector (names should correspond to the levels of factors). Advisable to supply here color list returned by sample_annotation_to_colors

annotation_color_rows

list of color vectors for row annotation, for each factor to be plotted; for factor-like variables a named vector (names should correspond to the levels of factors). Advisable to supply here color list returned by sample_annotation_to_colors

fill_the_missing

numeric value that the missing values are substituted with, or NULL if features with missing values are to be excluded.

color_for_missing

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

heatmap_color

vector of colors used in heatmap (typicall a gradient)

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))

...

other parameters of link[pheatmap]{pheatmap}

Value

pheatmap-type object

Examples

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p <- plot_heatmap_generic(log_transform_dm(example_proteome_matrix), 
column_annotation_df = example_sample_annotation,
columns_for_cols = c("MS_batch",  "digestion_batch", "Diet", 'DateTime'),
plot_title = 'test_heatmap',
show_rownames = FALSE, show_colnames = FALSE)

proBatch documentation built on Nov. 8, 2020, 4:55 p.m.