HeatmapAtomic {plotthis} | R Documentation |
Atomic heatmap without split
Description
Atomic heatmap without split
Usage
HeatmapAtomic(
data,
values_by,
values_fill = NA,
rows_by = NULL,
rows_split_by = NULL,
columns_by = NULL,
columns_split_by = NULL,
palette = "RdBu",
palcolor = NULL,
rows_palette = "Paired",
rows_palcolor = NULL,
rows_split_palette = "simspec",
rows_split_palcolor = NULL,
columns_palette = "Paired",
columns_palcolor = NULL,
columns_split_palette = "simspec",
columns_split_palcolor = NULL,
pie_size_name = "size",
pie_size = NULL,
pie_values = "length",
pie_group_by = NULL,
pie_palette = "Spectral",
pie_palcolor = NULL,
bars_sample = 100,
label = identity,
label_size = 10,
violin_fill = NULL,
boxplot_fill = NULL,
dot_size = 8,
dot_size_name = "size",
legend_items = NULL,
legend_discrete = FALSE,
legend.position = "right",
legend.direction = "vertical",
lower_quantile = 0,
upper_quantile = 0.99,
lower_cutoff = NULL,
upper_cutoff = NULL,
add_bg = FALSE,
bg_alpha = 0.5,
add_reticle = FALSE,
reticle_color = "grey",
column_name_annotation = TRUE,
column_name_legend = NULL,
row_name_annotation = TRUE,
row_name_legend = NULL,
cluster_columns = TRUE,
cluster_rows = TRUE,
show_row_names = !row_name_annotation,
show_column_names = !column_name_annotation,
border = TRUE,
title = NULL,
column_title = character(0),
row_title = character(0),
na_col = "grey85",
row_names_side = "right",
column_names_side = "bottom",
column_annotation = NULL,
column_annotation_side = "top",
column_annotation_palette = "Paired",
column_annotation_palcolor = NULL,
column_annotation_type = "auto",
column_annotation_params = list(),
column_annotation_agg = NULL,
row_annotation = NULL,
row_annotation_side = "left",
row_annotation_palette = "Paired",
row_annotation_palcolor = NULL,
row_annotation_type = "auto",
row_annotation_params = list(),
row_annotation_agg = NULL,
flip = FALSE,
alpha = 1,
seed = 8525,
return_grob = FALSE,
layer_fun_callback = NULL,
cell_type = "tile",
cell_agg = NULL,
...
)
Arguments
data |
A data frame used to create the heatmap. The data should be in a long form where each row represents a instance in the heatmap. |
values_by |
A character of column name in |
values_fill |
A value to fill in the missing values in the heatmap. When there is missing value in the data, the cluster_rows and cluster_columns will fail. |
rows_by |
A vector of column names in |
rows_split_by |
A character of column name in |
columns_by |
A vector of column names in |
columns_split_by |
A character of column name in |
palette |
A character string specifying the palette of the heatmap cells. |
palcolor |
A character vector of colors to override the palette of the heatmap cells. |
rows_palette |
A character string specifying the palette of the row group annotation. The default is "Paired". |
rows_palcolor |
A character vector of colors to override the palette of the row group annotation. |
rows_split_palette |
A character string specifying the palette of the row split annotation. The default is "simspec". |
rows_split_palcolor |
A character vector of colors to override the palette of the row split annotation. |
columns_palette |
A character string specifying the palette of the column group annotation. The default is "Paired". |
columns_palcolor |
A character vector of colors to override the palette of the column group annotation. |
columns_split_palette |
A character string specifying the palette of the column split annotation. The default is "simspec". |
columns_split_palcolor |
A character vector of colors to override the palette of the column split annotation. |
pie_size_name |
A character string specifying the name of the legend for the pie size. |
pie_size |
A numeric value or a function specifying the size of the pie chart.
If it is a function, the function should take |
pie_values |
A function or character that can be converted to a function by |
pie_group_by |
A character of column name in |
pie_palette |
A character string specifying the palette of the pie chart. |
pie_palcolor |
A character vector of colors to override the palette of the pie chart. |
bars_sample |
An integer specifying the number of samples to draw the bars. |
label |
A function to calculate the labels for the heatmap cells. It takes the aggregated values as the argument and returns the labels to be shown in the heatmap. No labels will be shown for the NA the returned values. |
label_size |
A numeric value specifying the size of the labels when |
violin_fill |
A character vector of colors to override the fill color of the violin plot. If NULL, the fill color will be the same as the annotion. |
boxplot_fill |
A character vector of colors to override the fill color of the boxplot. If NULL, the fill color will be the same as the annotion. |
dot_size |
A numeric value specifying the size of the dot or a function to calculate the size from the values in the cell or a function to calculate the size from the values in the cell. |
dot_size_name |
A character string specifying the name of the legend for the dot size. If NULL, the dot size legend will not be shown. |
legend_items |
A numeric vector with names to specifiy the items in the main legend. The names will be working as the labels of the legend items. |
legend_discrete |
A logical value indicating whether the main legend is discrete. |
legend.position |
A character string specifying the position of the legend.
if |
legend.direction |
A character string specifying the direction of the legend. |
lower_quantile , upper_quantile , lower_cutoff , upper_cutoff |
Vector of minimum and maximum cutoff values or quantile values for each feature. It's applied to aggregated values when aggregated values are used (e.g. plot_type tile, label, etc). It's applied to raw values when raw values are used (e.g. plot_type bars, etc). |
add_bg |
A logical value indicating whether to add a background to the heatmap.
Does not work with |
bg_alpha |
A numeric value between 0 and 1 specifying the transparency of the background. |
add_reticle |
A logical value indicating whether to add a reticle to the heatmap. |
reticle_color |
A character string specifying the color of the reticle. |
column_name_annotation |
A logical value indicating whether to add the column annotation for the column names. which is a simple annotaion indicating the column names. |
column_name_legend |
A logical value indicating whether to show the legend of the column name annotation. |
row_name_annotation |
A logical value indicating whether to add the row annotation for the row names. which is a simple annotaion indicating the row names. |
row_name_legend |
A logical value indicating whether to show the legend of the row name annotation. |
cluster_columns |
A logical value indicating whether to cluster the columns. If TRUE and columns_split_by is provided, the clustering will only be applied to the columns within the same split. |
cluster_rows |
A logical value indicating whether to cluster the rows. If TRUE and rows_split_by is provided, the clustering will only be applied to the rows within the same split. |
show_row_names |
A logical value indicating whether to show the row names. If TRUE, the legend of the row group annotation will be hidden. |
show_column_names |
A logical value indicating whether to show the column names. If TRUE, the legend of the column group annotation will be hidden. |
border |
A logical value indicating whether to draw the border of the heatmap. If TRUE, the borders of the slices will be also drawn. |
title |
The global (column) title of the heatmap |
column_title |
A character string/vector of the column name(s) to use as the title of the column group annotation. |
row_title |
A character string/vector of the column name(s) to use as the title of the row group annotation. |
na_col |
A character string specifying the color for missing values. The default is "grey85". |
row_names_side |
A character string specifying the side of the row names. The default is "right". |
column_names_side |
A character string specifying the side of the column names. The default is "bottom". |
column_annotation |
A character string/vector of the column name(s) to use as the column annotation. Or a list with the keys as the names of the annotation and the values as the column names. |
column_annotation_side |
A character string specifying the side of the column annotation. Could be a list with the keys as the names of the annotation and the values as the sides. |
column_annotation_palette |
A character string specifying the palette of the column annotation. The default is "Paired". Could be a list with the keys as the names of the annotation and the values as the palettes. |
column_annotation_palcolor |
A character vector of colors to override the palette of the column annotation. Could be a list with the keys as the names of the annotation and the values as the palcolors. |
column_annotation_type |
A character string specifying the type of the column annotation. The default is "auto". Other options are "simple", "pie", "ring", "bar", "violin", "boxplot", "density". Could be a list with the keys as the names of the annotation and the values as the types. If the type is "auto", the type will be determined by the type and number of the column data. |
column_annotation_params |
A list of parameters passed to the annotation function. Could be a list with the keys as the names of the annotation and the values as the parameters. |
column_annotation_agg |
A function to aggregate the values in the column annotation. |
row_annotation |
A character string/vector of the column name(s) to use as the row annotation. Or a list with the keys as the names of the annotation and the values as the column names. |
row_annotation_side |
A character string specifying the side of the row annotation. Could be a list with the keys as the names of the annotation and the values as the sides. |
row_annotation_palette |
A character string specifying the palette of the row annotation. The default is "Paired". Could be a list with the keys as the names of the annotation and the values as the palettes. |
row_annotation_palcolor |
A character vector of colors to override the palette of the row annotation. Could be a list with the keys as the names of the annotation and the values as the palcolors. |
row_annotation_type |
A character string specifying the type of the row annotation. The default is "auto". Other options are "simple", "pie", "ring", "bar", "violin", "boxplot", "density". Could be a list with the keys as the names of the annotation and the values as the types. If the type is "auto", the type will be determined by the type and number of the row data. |
row_annotation_params |
A list of parameters passed to the annotation function. Could be a list with the keys as the names of the annotation and the values as the parameters. |
row_annotation_agg |
A function to aggregate the values in the row annotation. |
flip |
A logical value indicating whether to flip the heatmap.
The idea is that, you can simply set |
alpha |
A numeric value between 0 and 1 specifying the transparency of the heatmap cells. |
seed |
The random seed to use. Default is 8525. |
return_grob |
A logical value indicating whether to return the grob object of the heatmap. This is useful when merging multiple heatmaps using patchwork. |
layer_fun_callback |
A function to add additional layers to the heatmap.
The function should have the following arguments: |
cell_type |
A character string specifying the type of the heatmap cells.
The default is values. Other options are "bars", "label", "dot", "violin", "boxplot".
Note that for pie chart, the values under columns specified by |
cell_agg |
A function to aggregate the values in the cell, for the cell type "tile" and "label".
The default is |
... |
Other arguments passed to |
Value
A drawn HeatmapList object if return_grob = FALSE
. Otherwise, a grob/gTree object.