plot_heatmap: Plots a heatmap

In kazeera/hourglass: This Package Provides Visualizations of Annotated Numeric Data

Plots a heatmap

Description

Transforms a numeric data frame/matrix and plots corresponding heatmap using the pheatmap function and saves to file

Usage

plot_heatmap(
  mat,
  ann_row = NA,
  ann_col = NA,
  ann_colors = NA,
  plot_title = "",
  out_dir = ".",
  labels = "",
  clust_row = F,
  clust_col = F,
  fontsize_col = 7,
  log10 = F,
  z_score = F,
  man_scale = T,
  man_scale_range = c(-2, 2),
  scale_func = F,
  col.or.row = 2,
  pheatmap_scale = "none",
  clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean",
  clustering_method = "complete",
  show_colnames = T,
  show_rownames = F,
  gradient_palette = "RdBu",
  border_color = NA,
  ...
)

Arguments

mat	Numeric matrix or data frame directory.
ann_row	A data frame that defines annotations or features for rows of the data matrix. The row names should the same as the row names of the data matrix.
ann_col	A data frame that defines annotations or features for columns of the data matrix. The row names should the same as the column names of the data matrix.
ann_colors	A list that specifies annotation colors (each element is a named vector, where names are unique groups in annotations), names of list are the annotation names.
out_dir	The output directory where the plot will be saved, default is current working
labels	A character vector of at least length 1 that will be collapsed for file name.
clust_row	Logical indicating whether to cluster rows
clust_col	Logical indicating whether to cluster rows
log10	Logical indicating whether to log10-transform values before plotting
z_score	Logical indicating whether to plot z_scores
man_scale	Logical indicating whether to manually scale each row/column using rescale() from scales package
man_scale_range	Numeric vector of length 2 indicating desired range of values e.g. c(-4,4), applied when man_scale is TRUE.
scale_func	Logical indicating whether to scale matrix using scale()
col.or.row	numeric - 1 for row, 2 for column. Only applicable when z_score, scale_func, man_scale are TRUE.
pheatmap_scale	String describing which direction around the mean to scale by. Accepts the same values ("none", "row", "column") as scale parameter in ?pheatmap
clustering_distance_rows	Distance measure to be used for row clustering. Accepts the same values as method parameter in ?dist.
clustering_distance_cols	Distance measure to be used for column clustering. Accepts the same values as method parameter in ?dist.
clustering_method	The agglomeration/clustering method to be used. Accepts the same values as method parameter in ?hclust.
show_colnames	Logical indicating whether to show column names on heatmap. See ?pheatmap
show_rownames	Logical indicating whether to show row names on heatmap. See ?pheatmap
gradient_palette	RColorBrewer palette. See RColorBrewer::display.brewer.all() for all options.
...	Additional plotting parameters. Parameters passed to pheatmap, see ?pheatmap.

See Also

Other plotting: plot_corrplot(), plot_corrplotgg(), plot_discrete_barplot(), plot_het_barplot(), plot_indiv_boxplot(), plot_indiv_corrscatt(), plot_indiv_paired(), plot_overview_boxplot(), plot_overview_corr_scatt(), plot_profile_barplot(), run_corrplot_analysis()

kazeera/hourglass documentation built on April 5, 2025, 7:18 a.m.