pheatmapwh: A modification of 'pheatmap' from the pheatmap package by...

In MalgorzataOles/BloodCancerMultiOmics2017: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis

A modification of pheatmap from the pheatmap package by Raivo Kolde: draw clustered heatmaps.

Description

A function to draw clustered heatmaps where one has better control over some graphical parameters such as cell size, etc.

Usage

pheatmapwh(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name =
  "RdYlBu")))(100), kmeans_k = NA, breaks = NA, border_color = "grey60",
  cellwidth = NA, cellheight = NA, scale = "none", cluster_rows = TRUE,
  cluster_cols = TRUE, clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean", clustering_method = "complete",
  clustering_callback = identity2, cutree_rows = NA, cutree_cols = NA,
  treeheight_row = ifelse(cluster_rows, 50, 0),
  treeheight_col = ifelse(cluster_cols, 50, 0), legend = TRUE,
  legend_breaks = NA, legend_labels = NA, annotation_row = NA,
  annotation_col = NA, annotation = NA, annotation_colors = NA,
  annotation_legend = TRUE, drop_levels = TRUE, show_rownames = T,
  show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize,
  fontsize_col = fontsize, display_numbers = F, number_format = "%.2f",
  number_color = "grey30", fontsize_number = 0.8 * fontsize,
  gaps_row = NULL, gaps_col = NULL, labels_row = NULL,
  labels_col = NULL, filename = NA, width = NA, height = NA,
  silent = FALSE, ...)

Arguments

mat	numeric matrix of the values to be plotted.
color	vector of colors used in heatmap.
kmeans_k	the number of kmeans clusters to make, if we want to agggregate the rows before drawing heatmap. If NA then the rows are not aggregated.
breaks	a sequence of numbers that covers the range of values in mat and is one element longer than color vector. Used for mapping values to colors. Useful, if needed to map certain values to certain colors, to certain values. If value is NA then the breaks are calculated automatically.
border_color	color of cell borders on heatmap, use NA if no border should be drawn.
cellwidth	individual cell width in points. If left as NA, then the values depend on the size of plotting window.
cellheight	individual cell height in points. If left as NA, then the values depend on the size of plotting window.
scale	character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"
cluster_rows	boolean values determining if rows should be clustered,
cluster_cols	boolean values determining if columns should be clustered.
clustering_distance_rows	distance measure used in clustering rows. Possible values are "correlation" for Pearson correlation and all the distances supported by dist, such as "euclidean", etc. If the value is none of the above it is assumed that a distance matrix is provided.
clustering_distance_cols	distance measure used in clustering columns. Possible values the same as for clustering_distance_rows.
clustering_method	clustering method used. Accepts the same values as hclust.
clustering_callback	callback function to modify the clustering. Is called with two parameters: original hclust object and the matrix used for clustering. Must return a hclust object.
cutree_rows	number of clusters the rows are divided into, based on the hierarchical clustering (using cutree), if rows are not clustered, the argument is ignored
cutree_cols	similar to cutree_rows, but for columns
treeheight_row	the height of a tree for rows, if these are clustered. Default value 50 points.
treeheight_col	the height of a tree for columns, if these are clustered. Default value 50 points.
legend	logical to determine if legend should be drawn or not.
legend_breaks	vector of breakpoints for the legend.
legend_labels	vector of labels for the legend_breaks.
annotation_row	data frame that specifies the annotations shown on left side of the heatmap. Each row defines the features for a specific row. The rows in the data and in the annotation are matched using corresponding row names. Note that color schemes takes into account if variable is continuous or discrete.
annotation_col	similar to annotation_row, but for columns.
annotation	deprecated parameter that currently sets the annotation_col if it is missing
annotation_colors	list for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features. Check examples for details.
annotation_legend	boolean value showing if the legend for annotation tracks should be drawn.
drop_levels	logical to determine if unused levels are also shown in the legend
show_rownames	boolean specifying if column names are be shown.
show_colnames	boolean specifying if column names are be shown.
main	the title of the plot
fontsize	base fontsize for the plot
fontsize_row	fontsize for rownames (Default: fontsize)
fontsize_col	fontsize for colnames (Default: fontsize)
display_numbers	logical determining if the numeric values are also printed to the cells. If this is a matrix (with same dimensions as original matrix), the contents of the matrix are shown instead of original values.
number_format	format strings (C printf style) of the numbers shown in cells. For example "%.2f" shows 2 decimal places and "%.1e" shows exponential notation (see more in sprintf).
number_color	color of the text
fontsize_number	fontsize of the numbers displayed in cells
gaps_row	vector of row indices that show shere to put gaps into heatmap. Used only if the rows are not clustered. See cutree_row to see how to introduce gaps to clustered rows.
gaps_col	similar to gaps_row, but for columns.
labels_row	custom labels for rows that are used instead of rownames.
labels_col	similar to labels_row, but for columns.
filename	file path where to save the picture. Filetype is decided by the extension in the path. Currently following formats are supported: png, pdf, tiff, bmp, jpeg. Even if the plot does not fit into the plotting window, the file size is calculated so that the plot would fit there, unless specified otherwise.
width	manual option for determining the output file width in inches.
height	manual option for determining the output file height in inches.
silent	do not draw the plot (useful when using the gtable output)
...	graphical parameters for the text used in plot. Parameters passed to grid.text, see gpar.

Details

The function also allows to aggregate the rows using kmeans clustering. This is advisable if number of rows is so big that R cannot handle their hierarchical clustering anymore, roughly more than 1000. Instead of showing all the rows separately one can cluster the rows in advance and show only the cluster centers. The number of clusters can be tuned with parameter kmeans_k.

Value

Invisibly a list of components

• tree_row the clustering of rows as hclust object

• tree_col the clustering of columns as hclust object

• kmeans the kmeans clustering of rows if parameter kmeans_k was specified

Author(s)

Raivo Kolde <[e-mail]>

Examples

# Create test matrix
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

# Draw heatmaps
pheatmapwh(test)
pheatmapwh(test, kmeans_k = 2)
pheatmapwh(test, scale = "row", clustering_distance_rows = "correlation")
pheatmapwh(test, color = colorRampPalette(c("navy", "white", "firebrick3"))(50))
pheatmapwh(test, cluster_row = FALSE)
pheatmapwh(test, legend = FALSE)

# Show text within cells
pheatmapwh(test, display_numbers = TRUE)
pheatmapwh(test, display_numbers = TRUE, number_format = "\%.1e")
pheatmapwh(test, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))
pheatmapwh(test, cluster_row = FALSE, legend_breaks = -1:4, legend_labels = c("0",
"1e-4", "1e-3", "1e-2", "1e-1", "1"))

# Fix cell sizes and save to file with correct size
pheatmapwh(test, cellwidth = 15, cellheight = 12, main = "Example heatmap")
pheatmapwh(test, cellwidth = 15, cellheight = 12, fontsize = 8, filename = "test.pdf")

# Generate annotations for rows and columns
annotation_col = data.frame(
                    CellType = factor(rep(c("CT1", "CT2"), 5)),
                    Time = 1:5
                )
rownames(annotation_col) = paste("Test", 1:10, sep = "")

annotation_row = data.frame(
                    GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6)))
                )
rownames(annotation_row) = paste("Gene", 1:20, sep = "")

# Display row and color annotations
pheatmapwh(test, annotation_col = annotation_col)
pheatmapwh(test, annotation_col = annotation_col, annotation_legend = FALSE)
pheatmapwh(test, annotation_col = annotation_col, annotation_row = annotation_row)


# Specify colors
ann_colors = list(
    Time = c("white", "firebrick"),
    CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
    GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E")
)

pheatmapwh(test, annotation_col = annotation_col, annotation_colors = ann_colors, main = "Title")
pheatmapwh(test, annotation_col = annotation_col, annotation_row = annotation_row,
         annotation_colors = ann_colors)
pheatmapwh(test, annotation_col = annotation_col, annotation_colors = ann_colors[2])

# Gaps in heatmaps
pheatmapwh(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14))
pheatmapwh(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14),
         cutree_col = 2)

# Show custom strings as row/col names
labels_row = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "Il10", "Il15", "Il1b")

pheatmapwh(test, annotation_col = annotation_col, labels_row = labels_row)

# Specifying clustering from distance matrix
drows = dist(test, method = "minkowski")
dcols = dist(t(test), method = "minkowski")
pheatmapwh(test, clustering_distance_rows = drows, clustering_distance_cols = dcols)

# Modify ordering of the clusters using clustering callback option
callback = function(hc, mat){
    sv = svd(t(mat))$v[,1]
    dend = reorder(as.dendrogram(hc), wts = sv)
    as.hclust(dend)
}

pheatmapwh(test, clustering_callback = callback)

## Not run: 
# Same using dendsort package
library(dendsort)

callback = function(hc, ...){dendsort(hc)}
pheatmapwh(test, clustering_callback = callback)

## End(Not run)

MalgorzataOles/BloodCancerMultiOmics2017 documentation built on March 29, 2024, 2:29 p.m.