Draws gapped heatmap (gapmap) and gapped dendrograms using ggplot2 in [R].

Description

Functions for drawing gapped cluster heatmap with ggplot2

Details

This is a set of tools for drawing gapmaps using ggplot

gap_data extracts data from a dendrogram object. Make sure to convert hclust object to dendrogram object by calling as.dendrogram(). This method generates an object class gapdata, consisting of a list of data.frames. The general workflow is as following:

1. Hierarchical clustering hclust()

2. Convert the hclust output class into dendrogram by calling as.dendrogram()

3. Generate a gapped cluster heatmap by specifying a matrix and dendrogram objects for rows and columns in gapmap() function

Author(s)

Ryo Sakai ryo.sakai@esat.kuleuven.be

Make a gapdata class object

Description

This function generates a gapdata class object. This object is used for drawing dendrograms and heatmaps.

Usage

as.gapdata(d, segments, labels, ...)

Arguments

Value

the gapdata class object

Re-evaluate the position of branches

Description

This function reevaluate the position of branches based on the gaps calculated.

Usage

assign_branch_positions(d, verbose = FALSE, ...)

Arguments

Value

the reevaluated dendrogram object

Re-evaluate the position of leaves

Description

This function reevaluate the position of leaves based on the gaps calculated.

Usage

assign_positions(d, runningX = 1, verbose = FALSE, ...)

Arguments

Value

the reevaluated dendrogram object

Calculate the gaps based on distance

Description

This function takes a dendrogram class object and other attributes to calcuate the size of gaps between leaves. The gap is stored in a leaf to its left. The function is called recursively.

Usage

calculate_gap(
  d,
  sum,
  gap_total,
  mode = c("quantitative", "threshold"),
  mapping = c("exponential", "linear"),
  scale = 0.2,
  max_height = 0,
  threshold = 2,
  gap_size = 0,
  verbose = FALSE,
  ...
)

Arguments

Value

the annotated dendrogram class object

Count the number of gaps based on a threshold

Description

This function counts the number of gaps based on the cutting the tree method. It counts the number of branches that are above the threshold distance.

Usage

count_gap(d = d, count = 0, threshold = threshold)

Arguments

Value

the count of gaps

Extract a list from the dendrogram object

Description

This function extract list of data.frames for drawing dendrograms

Usage

extract_list(d, type, segments_df = NULL, labels_df = NULL, ...)

Arguments

Value

the extracted list

Function to format a number

Description

This function takes a floating number and round to 2 decimal point

Usage

format_number(x)

Arguments

Value

formatted number

Generate a gapdata class object from a dendrogram object

Description

This function takes a dendrogram class object as an input, and generate a gapdata class object as an output. By parsing the dendrogram object based on parameters for gaps, gaps between leaves in a dendrogram are introduced, and the coordinates of the leaves are adjusted. The gaps can be based on the a height (or distance) threshold to to introduce the gaps of the same width, or quantitative mapping of distance values mapped linearly or exponentially.

Usage

gap_data(
  d,
  mode = c("quantitative", "threshold"),
  mapping = c("exponential", "linear"),
  ratio = 0.2,
  scale = 0.5,
  threshold = 0,
  verbose = FALSE,
  ...
)

Arguments

Value

a list of data frames that contain coordinates for drawing a gapped dendrogram

Function to draw a gapped dendrogram

Description

This function draws a gapped dendrogram using the ggplot2 package. The input for the function is the gapdata class object, generated from gap_data() function.

Usage

gap_dendrogram(
  data,
  leaf_labels = TRUE,
  rotate_label = FALSE,
  orientation = c("top", "right", "bottom", "left"),
  ...
)

Arguments

Value

a ggplot object

Function to draw a gapped heatmap

Description

This function draws a gapped heatmap using the ggplot2 package. The input for the function are the gapdata class objects, generated from gap_data() function, and the data matrix.

Usage

gap_heatmap(
  m,
  row_gap = NULL,
  col_gap = NULL,
  row_labels = TRUE,
  col_labels = TRUE,
  rotate = FALSE,
  col = c("#053061", "#2166AC", "#4393C3", "#92C5DE", "#D1E5F0", "#F7F7F7", "#FDDBC7",
    "#F4A582", "#D6604D", "#B2182B", "#67001F")
)

Arguments

Value

a ggplot object

Function to draw a gapped labels

Description

This function draws a gapped labels using the ggplot2 package. The input for the function is the gapdata class object, generated from gap_data() function.

Usage

gap_label(data, orientation, label_size = 5)

Arguments

Value

a ggplot object

Function to draw a gapped cluster heatmap

Description

This function draws a gapped cluster heatmap using the ggplot2 package. The input for the function is the a matrix, two dendrograms, and parameters for gaps.

Usage

gapmap(
  m,
  d_row,
  d_col,
  mode = c("quantitative", "threshold"),
  mapping = c("exponential", "linear"),
  ratio = 0.2,
  scale = 0.5,
  threshold = 0,
  row_threshold = NULL,
  col_threshold = NULL,
  rotate_label = TRUE,
  verbose = FALSE,
  left = "dendrogram",
  top = "dendrogram",
  right = "label",
  bottom = "label",
  col = c("#053061", "#2166AC", "#4393C3", "#92C5DE", "#D1E5F0", "#F7F7F7", "#FDDBC7",
    "#F4A582", "#D6604D", "#B2182B", "#67001F"),
  h_ratio = c(0.2, 0.7, 0.1),
  v_ratio = c(0.2, 0.7, 0.1),
  label_size = 5,
  show_legend = FALSE,
  ...
)

Arguments

Value

a ggplot object

Examples

set.seed(1234)
#generate sample data
x <- rnorm(10, mean=rep(1:5, each=2), sd=0.4)
y <- rnorm(10, mean=rep(c(1,2), each=5), sd=0.4)
dataFrame <- data.frame(x=x, y=y, row.names=c(1:10))
#calculate distance matrix. default is Euclidean distance
distxy <- dist(dataFrame)
#perform hierarchical clustering. default is complete linkage.
hc <- hclust(distxy)
dend <- as.dendrogram(hc)
#make a cluster heatmap plot
gapmap(m = as.matrix(distxy), d_row= rev(dend), d_col=dend)

Get the most left leaf object from a dendrogram

Description

This function returns the most left leaf object.

Usage

get_most_left_leaf(d)

Arguments

Value

the most left leaf object

Get the most right leaf object from a dendrogram

Description

This function returns the most right leaf object.

Usage

get_most_right_leaf(d)

Arguments

Value

the most right leaf object

Make a data.frame object

Description

This function just make a data.frame based on 4 input parameters

Usage

get_segment_df(x0, y0, x1, y1)

Arguments

Value

A data.frame

Function to check if a object is a gapdata class object

Description

This function checks if a object is a gapdata class object.

Usage

is.gapdata(x)

Arguments

Value

a logical TRUE or FALSE

A function to map values in a range

Description

This function maps a value in one range to another range.

Usage

map(value, start1, stop1, start2, stop2)

Arguments

Value

a numeric value

A function to map values in a range exponentially

Description

This function maps a value in one range to another range exponentially.

Usage

map.exp(value, start1, stop1, start2, stop2, scale = 0.5)

Arguments

Value

a numeric value

Sample data matrix from the integrated pathway analysis of gastric cancer from the Cancer Genome Atlas (TCGA) study.

Description

a multivariate table obtained from the integrated pathway analysis of gastric cancer from the Cancer Genome Atlas (TCGA) study. In this data set, each column represents a pathway consisting of a set of genes and each row represents a cohort of samples based on specific clinical or genetic features. For each pair of a pathway and a feature, a continuous value of between 1 and -1 is assigned to score positive or negative association, respectively.

Usage

data(sample_tcga)

Format

A data frame with 215 rows and 117 variables

Details

We would like to thank Sheila Reynolds and Vesteinn Thorsson from the Institute for Systems Biology for sharing this sample data set.

Set the most right leaf object from a dendrogram

Description

This function replace the most right leaf with provided dendrogram

Usage

set_most_right_leaf(d, d2, ...)

Arguments

Value

the dendrogram class object where the most right leaf is replaced

Sum the distance of all branches in a dendrogram

Description

This function takes a dendrogram class object as an input, and adds up all the distances of branches. This function is called recursively to adds up the sum. In case of exponential mapping for the quantitative mode, the sum is in the exponential scale

Usage

sum_distance(
  d,
  sum = 0,
  mapping = c("exponential", "linear"),
  scale = 0,
  max_height = 0,
  ...
)

Arguments

Value

the sum of distances