Heatmap {ComplexHeatmap} | R Documentation |
Constructor method for Heatmap class
Heatmap(matrix, col, name, na_col = "grey", color_space = "LAB", rect_gp = gpar(col = NA), border = NA, cell_fun = NULL, layer_fun = NULL, jitter = FALSE, row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 14), row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 14), column_title_rot = 0, cluster_rows = TRUE, cluster_row_slices = TRUE, clustering_distance_rows = "euclidean", clustering_method_rows = "complete", row_dend_side = c("left", "right"), row_dend_width = unit(10, "mm"), show_row_dend = TRUE, row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows), row_dend_gp = gpar(), cluster_columns = TRUE, cluster_column_slices = TRUE, clustering_distance_columns = "euclidean", clustering_method_columns = "complete", column_dend_side = c("top", "bottom"), column_dend_height = unit(10, "mm"), show_column_dend = TRUE, column_dend_gp = gpar(), column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns), row_order = NULL, column_order = NULL, row_labels = rownames(matrix), row_names_side = c("right", "left"), show_row_names = TRUE, row_names_max_width = unit(6, "cm"), row_names_gp = gpar(fontsize = 12), row_names_rot = 0, row_names_centered = FALSE, column_labels = colnames(matrix), column_names_side = c("bottom", "top"), show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, column_names_centered = FALSE, top_annotation = NULL, bottom_annotation = NULL, left_annotation = NULL, right_annotation = NULL, km = 1, split = NULL, row_km = km, row_km_repeats = 1, row_split = split, column_km = 1, column_km_repeats = 1, column_split = NULL, gap = unit(1, "mm"), row_gap = unit(1, "mm"), column_gap = unit(1, "mm"), show_parent_dend_line = ht_opt$show_parent_dend_line, heatmap_width = unit(1, "npc"), width = NULL, heatmap_height = unit(1, "npc"), height = NULL, show_heatmap_legend = TRUE, heatmap_legend_param = list(title = name), use_raster = NULL, raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"), raster_quality = 2, raster_device_param = list(), raster_resize = FALSE, post_fun = NULL)
matrix |
A matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix. |
col |
A vector of colors if the color mapping is discrete or a color mapping function if the matrix is continuous numbers (should be generated by |
name |
Name of the heatmap. By default the heatmap name is used as the title of the heatmap legend. |
na_col |
Color for |
rect_gp |
Graphic parameters for drawing rectangles (for heatmap body). The value should be specified by |
color_space |
The color space in which colors are interpolated. Only used if |
border |
Whether draw border. The value can be logical or a string of color. |
cell_fun |
Self-defined function to add graphics on each cell. Seven parameters will be passed into this function: |
layer_fun |
Similar as |
jitter |
Random shifts added to the matrix. The value can be logical or a single numeric value. It it is |
row_title |
Title on the row. |
row_title_side |
Will the title be put on the left or right of the heatmap? |
row_title_gp |
Graphic parameters for row title. |
row_title_rot |
Rotation of row title. Only 0, 90, 270 are allowed to set. |
column_title |
Title on the column. |
column_title_side |
Will the title be put on the top or bottom of the heatmap? |
column_title_gp |
Graphic parameters for column title. |
column_title_rot |
Rotation of column titles. Only 0, 90, 270 are allowed to set. |
cluster_rows |
If the value is a logical, it controls whether to make cluster on rows. The value can also be a |
cluster_row_slices |
If rows are split into slices, whether perform clustering on the slice means? |
clustering_distance_rows |
It can be a pre-defined character which is in ("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and the returned value should be a |
clustering_method_rows |
Method to perform hierarchical clustering, pass to |
row_dend_side |
Should the row dendrogram be put on the left or right of the heatmap? |
row_dend_width |
Width of the row dendrogram, should be a |
show_row_dend |
Whether show row dendrogram? |
row_dend_gp |
Graphic parameters for the dendrogram segments. If users already provide a |
row_dend_reorder |
Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight which is used to reorder rows. The reordering is applied by |
cluster_columns |
Whether make cluster on columns? Same settings as |
cluster_column_slices |
If columns are split into slices, whether perform clustering on the slice means? |
clustering_distance_columns |
Same setting as |
clustering_method_columns |
Method to perform hierarchical clustering, pass to |
column_dend_side |
Should the column dendrogram be put on the top or bottom of the heatmap? |
column_dend_height |
height of the column cluster, should be a |
show_column_dend |
Whether show column dendrogram? |
column_dend_gp |
Graphic parameters for dendrogram segments. Same settings as |
column_dend_reorder |
Apply reordering on column dendrograms. Same settings as |
row_order |
Order of rows. Manually setting row order turns off clustering. |
column_order |
Order of column. |
row_labels |
Optional row labels which are put as row names in the heatmap. |
row_names_side |
Should the row names be put on the left or right of the heatmap? |
show_row_names |
Whether show row names. |
row_names_max_width |
Maximum width of row names viewport. |
row_names_gp |
Graphic parameters for row names. |
row_names_rot |
Rotation of row names. |
row_names_centered |
Should row names put centered? |
column_labels |
Optional column labels which are put as column names in the heatmap. |
column_names_side |
Should the column names be put on the top or bottom of the heatmap? |
column_names_max_height |
Maximum height of column names viewport. |
show_column_names |
Whether show column names. |
column_names_gp |
Graphic parameters for drawing text. |
column_names_rot |
Rotation of column names. |
column_names_centered |
Should column names put centered? |
top_annotation |
A |
bottom_annotation |
A |
left_annotation |
It should be specified by |
right_annotation |
it should be specified by |
km |
Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above. |
split |
A vector or a data frame by which the rows are split. But if |
row_km |
Same as |
row_km_repeats |
Number of k-means runs to get a consensus k-means clustering. Note if |
row_split |
Same as |
column_km |
K-means clustering on columns. |
column_km_repeats |
Number of k-means runs to get a consensus k-means clustering. Similar as |
column_split |
Split on columns. For heatmap splitting, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split . |
gap |
Gap between row slices if the heatmap is split by rows. The value should be a |
row_gap |
Same as |
column_gap |
Gap between column slices. |
show_parent_dend_line |
When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms? |
width |
Width of the heatmap body. |
height |
Height of the heatmap body. |
heatmap_width |
Width of the whole heatmap (including heatmap components) |
heatmap_height |
Height of the whole heatmap (including heatmap components). Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#size-of-the-heatmap . |
show_heatmap_legend |
Whether show heatmap legend? |
heatmap_legend_param |
A list contains parameters for the heatmap legends. See |
use_raster |
Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if |
raster_device |
Graphic device which is used to generate the raster image. |
raster_quality |
A value set to larger than 1 will improve the quality of the raster image. |
raster_device_param |
A list of further parameters for the selected graphic device. For raster image support, please check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image . |
raster_resize |
Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? |
post_fun |
A function which will be executed after the heatmap list is drawn. |
The initialization function only applies parameter checking and fill values to the slots with some validation.
Following methods can be applied to the Heatmap-class
object:
show,Heatmap-method
: draw a single heatmap with default parameters
draw,Heatmap-method
: draw a single heatmap.
+
or %v%
append heatmaps and annotations to a list of heatmaps.
The constructor function pretends to be a high-level graphic function because the show
method
of the Heatmap-class
object actually plots the graphics.
A Heatmap-class
object.
Zuguang Gu <z.gu@dkfz.de>
https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html
# There is no example NULL