add_iheatmap {iheatmapr}

add_iheatmap

Description

add_iheatmap

Usage

## S4 method for signature 'IheatmapHorizontal,matrix'
add_iheatmap(
  p,
  data,
  x = default_x(data),
  cluster_cols = c("none", "hclust", "kmeans", "groups"),
  col_clusters = NULL,
  col_k = NULL,
  col_clust_dist = stats::dist,
  name = "Signal",
  scale = c("none", "rows", "cols"),
  scale_method = c("standardize", "center", "normalize"),
  colors = NULL,
  col_clusters_colors = NULL,
  col_clusters_name = "Col<br>Clusters",
  show_col_clusters_colorbar = TRUE,
  row_annotation = NULL,
  col_annotation = NULL,
  row_annotation_colors = NULL,
  col_annotation_colors = NULL,
  row_labels = NULL,
  col_labels = NULL,
  row_title = NULL,
  col_title = NULL,
  buffer = 0.2,
  ...
)

## S4 method for signature 'IheatmapVertical,matrix'
add_iheatmap(
  p,
  data,
  y = default_y(data),
  cluster_rows = c("none", "hclust", "kmeans", "groups"),
  row_clusters = NULL,
  row_k = NULL,
  row_clust_dist = stats::dist,
  name = "Signal",
  scale = c("none", "rows", "cols"),
  scale_method = c("standardize", "center", "normalize"),
  colors = NULL,
  row_clusters_colors = NULL,
  row_clusters_name = "Col<br>Clusters",
  show_row_clusters_colorbar = TRUE,
  row_annotation = NULL,
  col_annotation = NULL,
  row_annotation_colors = NULL,
  col_annotation_colors = NULL,
  row_labels = NULL,
  col_labels = NULL,
  row_title = NULL,
  col_title = NULL,
  buffer = 0.2,
  ...
)

Arguments

p

iheatmap object

data

matrix of values to be plotted as heatmap

x

x xaxis labels, by default colnames of data

cluster_cols

"none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of columnsrespectively

col_clusters

vector of pre-determined column cluster assignment

col_k

number of clusters for columns, needed if cluster_rows is kmeans or optional if hclust

col_clust_dist

distance function to use for column clustering if hierarchical clustering

name

Name for colorbar

scale

scale matrix by rows, cols or none

scale_method

what method to use for scaling, either standardize, center, normalize

colors

name of RColorBrewer palette or vector of colors for main heatmap

col_clusters_colors

colors for col clusters annotation heatmap

col_clusters_name

name for col clusters colorbar

show_col_clusters_colorbar

show the colorbar for column clusters?

row_annotation

row annotation data.frame

col_annotation

column annotation data.frame

row_annotation_colors

list of colors for row annotations heatmap

col_annotation_colors

list of colors for col annotations heatmap

row_labels

axis labels for y axis

col_labels

axis labels for x axis

row_title

x axis title

col_title

y axis title

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

...

additional argument to add_iheatmap

y

y axis labels, by default rownames of data

cluster_rows

"none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of rows respectively

row_clusters

vector of pre-determined row cluster assignment

row_k

number of clusters for rows, needed if cluster_rows is kmeans or optional if hclust

row_clust_dist

distance function to use for row clustering if hierarchical clustering

row_clusters_colors

colors for row clusters annotation heatmap

row_clusters_name

name for row clusters colorbar

show_row_clusters_colorbar

show the colorbar for row clusters?

Details

By default, no scaling is done of rows or columns. This can be changed by specifying the 'scale' argument. There are three options for scaling methods. "standardize" subtracts the mean and divides by standard deviation, "center" just subtracts the mean, and "normalize" divides by the sum of the values. "normalize" should only be used for data that is all positive! If alternative scaling is desired, the scaling should be done prior to calling the iheatmap function.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, main_heatmap

Examples

mat <- matrix(rnorm(24), nrow = 6)
mat2 <- matrix(rnorm(24), nrow = 6)
annotation = data.frame(gender = c(rep("M", 3),rep("F",3)),
                        age = c(20,34,27,19,23,30))
hm <- iheatmap(mat, 
 cluster_rows = "hclust", 
 cluster_cols = "hclust", 
 col_k = 3) %>%
add_iheatmap(mat2, 
 cluster_cols = "hclust", 
 col_k = 3, 
 row_annotation = annotation)

# Print heatmap if interactive session 
if (interactive()) hm