pav_heatmap: pav_heatmap

In xiaonui/vPan: An R package to analyze and visualize PAV results from pan-genome of "map-to-pan" strategy.

Description

pav_heatmap

Usage

pav_heatmap(
  pav_obj,
  gene_type,
  add_phen_info = NULL,
  add_gene_info = NULL,
  border = T,
  split_block = T,
  block_name_size = NULL,
  block_name_rot = 0,
  cluster_rows = F,
  clustering_distance_rows = "euclidean",
  clustering_method_rows = "complete",
  row_dend_side = "left",
  row_dend_width = grid::unit(5, "mm"),
  row_sorted = c(),
  show_row_names = F,
  row_names_side = "right",
  row_names_size = 10,
  row_names_rot = 0,
  cluster_columns = F,
  clustering_distance_columns = "euclidean",
  clustering_method_columns = "complete",
  column_dend_side = "top",
  column_dend_height = grid::unit(5, "mm"),
  column_sorted = c(),
  show_column_names = F,
  column_names_side = "bottom",
  column_names_size = 10,
  column_names_rot = 90,
  anno_param_row_phen = list(show = T, width = 5, border = F, name_size = NULL,
    name_rot = 90, name_side = "top"),
  anno_param_column_gene = list(show = T, height = 5, border = FALSE, name_size = NULL,
    name_rot = 0, name_side = "right"),
  anno_param_row_stat = list(show = T, width = 10, bar_width = 1, border = FALSE, title
    = "Presence\nNumber", title_size = 10, title_side = "bottom", title_rot = 0,
    axis_side = "bottom", axis_at = NULL, axis_labels = NULL, axis_labels_size = 8),
  anno_param_column_stat = list(show = T, height = 10, bar_width = 1, border = FALSE,
    title = "Presence\nNumber", title_size = 10, title_side = "left", title_rot = 0,
    axis_side = "left", axis_at = NULL, axis_labels = NULL, axis_labels_size = 8),
  pav_colors = c(presence = "steelblue", absence = "gray70"),
  type_colors = NULL,
  gene_info_color_list = NULL,
  phen_info_color_list = NULL,
  legend_side = "right",
  legend_title = list(pav = "PAV", type = "gene"),
  legend_title_size = NULL,
  legend_text_size = NULL,
  legend_grid_size = grid::unit(4, "mm"),
  use_raster = NULL
)

Arguments

pav_obj	A PAV object.
gene_type	A vector of gene types. These can be any of the following: "core", "softcore", "distributed" and "private".
add_phen_info	A character vector of 'phen_info' names.
add_gene_info	A character vector of 'gene_info' names.
border	A logical value or a string of color indicating whether draw border.
split_block	A logical value indicating whether split columns based on gene types.
block_name_size	The size of block name.
block_name_rot	The rotation of block name.
cluster_rows	A logical value indicating whether perform clustering on rows.
clustering_distance_rows	Method of measuring distance when clustring on rows, pass to dist.
clustering_method_rows	Method to perform hierarchical clustering on rows, pass to hclust.
row_dend_side	The position of the row dendrogram ("left", "right").
row_dend_width	A unit object for the width of the row dendrogram.
row_sorted	A vector of sorted row names. It only works when 'cluster_rows = F'.
show_row_names	A logical value indicating whether show row names.
row_names_side	The position of row names ("left", "right").
row_names_size	The size of row names.
row_names_rot	The rotation of row names.
cluster_columns	A logical value indicating whether perform clustering on columns.
clustering_distance_columns	Method of measuring distance when clustring on columns, pass to dist.
clustering_method_columns	Method to perform hierarchical clustering on columns, pass to hclust.
column_dend_side	The position of the column dendrogram ("top", "bottom").
column_dend_height	A unit object for the height of the column dendrogram.
column_sorted	A vector of sorted column names. It only works when 'cluster_columns = F' and 'split_block = F'.
show_column_names	A logical value indicating whether show column names.
column_names_side	The position of column names ("top", "column").
column_names_size	The size of column names.
column_names_rot	The rotation of column names.
anno_param_row_phen	A list contains parameters for the phenotype annotation. These can be any of the following: "show", "width", "border", "name_size", "name_rot" and "name_side".
anno_param_column_gene	A list contains parameters for the gene annotation. These can be any of the following: "show", "height", "border", "name_size", "name_rot" and "name_side".
anno_param_row_stat	A list contains parameters for the stat annotation of rows. These can be any of the following: "show", "width", "border", "title", "title_size", "title_rot", "title_side", "axis_side", "axis_at", "axis_labels" and "axis_labels_size".
anno_param_column_stat	A list contains parameters for the stat annotation of columns. These can be any of the following: "show", "height", "border", "title", "title_size", "title_rot", "title_side", "axis_side", "axis_at", "axis_labels" and "axis_labels_size".
pav_colors	A named vector of colors for presence and absence. e.g. c(presence = "steelblue", absence = "gray70")
type_colors	A named vector of colors for types. e.g. c("distributed" = "red")
gene_info_color_list	A list contains named vector of colors for 'gene_info' annotation. e.g. list(source = c("reference" = "red", "novel" = "blue"), length = c("orange", "red"))
phen_info_color_list	A list contains named vector of colors for 'phen_info' annotation. e.g. list(gender = c("Male" = "green", "Female" = "red"), age = c("yellow", "red"))
legend_side	The position of legend ("top", "bottom", "right", "left").
legend_title	The text for the legend title.
legend_title_size	The size of legend title.
legend_text_size	The size of legend item labels.
legend_grid_size	A unit object for the size of legend grid.
use_raster	Whether render the heatmap body as a raster image. pass to Heatmap

xiaonui/vPan documentation built on Dec. 23, 2021, 6:17 p.m.