Usage
pheatmap(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", 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 = TRUE, show_colnames = TRUE, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, display_numbers = FALSE, 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, legend.cex = 1, txt.stats = NA, ...)
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. 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)
legend.cex
Default 0.5; determines legend size if legend = TRUE
txt.stats
By default, shows a summary statistics for shown data (n,m, |G| and |P|)
...
graphical parameters for the text used in plot. Parameters passed to
grid.text, see gpar.