ggheatmap: Plots a ggplot heatmap
In csgroen/ggheatmapper: Tile-able heatmaps using ggheatmap and patchwork

View source: R/ggheatmap.R

ggheatmap

R Documentation

Plots a ggplot heatmap

Description

ggheatmap() is the main function of the ggheatmap package. It constructs a tile-able plot using ggplot and patchwork, that can be added to and used in constructing panels.

Usage

ggheatmap(
  table,
  colv = NULL,
  rowv = NULL,
  hm_colors = "RdYlBu",
  hm_color_values = NULL,
  hm_color_breaks = waiver(),
  hm_color_limits = NULL,
  scale = FALSE,
  center = FALSE,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  dist_method = "euclidean",
  clustering_method = "complete",
  raster = FALSE,
  rows_title = "",
  column_title = "",
  colors_title = "value",
  fontsize = 11,
  show_rownames = TRUE,
  show_colnames = TRUE,
  show_dend_row = TRUE,
  show_dend_col = TRUE,
  dend_lwd = 0.3,
  dend_prop_row = 0.1,
  dend_prop_col = 0.1,
  group_track = TRUE,
  group_label = FALSE,
  group_track_topslack = 0,
  group_label_angle = 0,
  group_label_size = 3.5,
  group_label_position = "center",
  group_prop = 0.1,
  group_colors = NULL,
  group_lines = FALSE,
  group_line_color = "black",
  group_lty = "solid",
  group_lwd = 0.3,
  group_leg_ncol = 3,
  row_facetting_space = 3,
  colorbar_dir = "vertical"
)

Arguments

`table`	A table that can follow four formats: If `table` is a `data.frame` or `tbl` and `colv` and `rowv` are provided, `colv` will be plotted into the columns (observations), while the variables provided as `rowv` will be plotted into the rows (variables). If `table` is a `grouped_tbl` and `cluster_cols = TRUE`, a semi-supervised clustering of the data will be performed instead only clustering within groups. If `table` is a `data.frame` or `tbl` and only `colv`, all other columns will be used as `rowv`. If `table` is a `matrix` or `data.frame` and `colv` and `rowv` are `NULL`, `ggheatmap` will plot it as-is (columns will be plotted as columns, rows as rows of the heatmap). It is convenient, but less powerful.
`colv`	Either NULL or the name of the column that contains the observation ID variable for the data.
`rowv`	Either NULL, a vector with names of columns to be plotted into the rows of the heatmap, or a named list of vectors for a faceted plot (`show_dend_row` will then be ignored).
`hm_colors`	Can be either: A valid palette used by `RColorBrewer`. See: `RColorBrewer::display.brewer.all()` A vector of colors to be interpolated
`hm_color_values`	Either NULL or a vector of values used for interpolation between colors. Passed to `values` from `ggplot2::scale_fill_gradientn()`
`hm_color_breaks`	Breaks for heatmap colors. Passed to `breaks` from `ggplot2::scale_fill_gradientn()`
`hm_color_limits`	A vector with length = 2 for limits of the heatmap color scale. Passed to `limits` from `ggplot2::scale_fill_gradientn()`.
`scale`	If TRUE, data will be scaled (z-score)
`center`	If TRUE, data will be centered
`cluster_rows`	If TRUE, rows will be clustered with `stats::hclust()`
`cluster_cols`	If TRUE, columns will be clustered with `stats::hclust()`
`dist_method`	Distance method passed to `stats::dist()`. Also supports correlation distance (`1-cor()`), with `dist_method` passed to method from `stats::cor`
`clustering_method`	Clustering method is passed to method from `stats::hclust()`
`raster`	If TRUE, `ggplot2::geom_raster()` will be used for the heatmap tiles instead of `ggplot2::geom_tile()`. Will be recommended by the function for large tables.
`rows_title`	A title for row variables.
`column_title`	A title for the column variable.
`colors_title`	A title for the color legend.
`fontsize`	Base fontsize for plot, which will be used by the theme. Ultimately passed to `ggplot2::theme_minimal()` as `base_size`.
`show_rownames`	If TRUE, row names will be shown in the heatmap.
`show_colnames`	If TRUE, column names will be shown in the heatmap.
`show_dend_row`	If TRUE, the clustering dendrogram for the row variables will be shown to the left of the heatmap
`show_dend_col`	If TRUE, the clustering dendrogram for the column variable will be shown on top of the heatmap.
`dend_lwd`	Linewidth for the dendrogram drawing. Passed to ggtree::ggtree as size.
`dend_prop_row`	A value between 0 and 1. The proportion of the width occupied by the dendrogram.
`dend_prop_col`	A value between 0 and 1. The proportion of the height occupied by the dendrogram.
`group_track`	If `table` is a `grouped_tbl` and `group_track = TRUE`, a track will be plot between the dendrogram and heatmap.
`group_label`	a logical indicating whether to label the groups directly. If TRUE, `show_dend_col` will be set to FALSE.
`group_track_topslack`	a numeric, indicating space to add at the top of the group track. Useful for fitting names
`group_label_angle`	an angle for the group labels
`group_label_size`	a numeric value to set the size of the group labels
`group_label_position`	one of: "left", "right" or "center", indicating where to write the group label if 'group_label = TRUE
`group_prop`	The proportion of the height of the heatmap that will be used for the group track.
`group_colors`	A named vector with colors for each level in the grouping variable. If NULL, automatic colors will be used.
`group_lines`	If TRUE, vertical lines will separate supervised clustering groups
`group_line_color`	Color of the vertical line
`group_lty`	Group line type. See graphics::par
`group_lwd`	Group line width. See graphics::par
`group_leg_ncol`	Number of columns in the groups legend. Passed to `ggplot2::guide_legend()`.
`row_facetting_space`	space in pts between row facets, if they exist
`colorbar_dir`	Places the `colorbar` either horizontal or vertically. See: ggplot2::guide_colorbar