# Flexible Heatmaps for Functional Genomics and Sequence Features

## Documentation for package ‘heatmaps’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

coords | Return or set the coords in a Heatmap
coords-method | Return or set the coords in a Heatmap
coords<- | Return or set the coords in a Heatmap
coords<--method | Return or set the coords in a Heatmap
CoverageHeatmap | Generate a Heatmap of coverage
CoverageHeatmap-method | Generate a Heatmap of coverage
default_color | Predifined color palettes from RColorBrewer + Rainbow
getScale | Make an appropriate scale for a heatmap
Heatmap | Function to create a heatmap object
Heatmap-class | An S4 class to represent a heatmap
HeatmapExamples | Data for man page examples
heatmapOptions | Generate default options for a Heatmap
hm | Data for man page examples
hm2 | Data for man page examples
image | Return or set the image in a Heatmap
image-method | Return or set the image in a Heatmap
image<- | Return or set the image in a Heatmap
image<--method | Return or set the image in a Heatmap
label | Return or set the label in a Heatmap
label-method | Return or set the label in a Heatmap
label<- | Return or set the label in a Heatmap
label<--method | Return or set the label in a Heatmap
length-method | Return the number of sequences in a heatmap
mat | Data for man page examples
metadata | Return or set the metadata in a Heatmap
metadata-method | Return or set the metadata in a Heatmap
metadata<- | Return or set the metadata in a Heatmap
metadata<--method | Return or set the metadata in a Heatmap
nseq | Return or set nseq in a Heatmap
nseq-method | Return or set nseq in a Heatmap
nseq<- | Return or set nseq in a Heatmap
nseq<--method | Return or set nseq in a Heatmap
PatternHeatmap | Generate a Heatmap of patterns in DNA sequence
PatternHeatmap-method | Generate a Heatmap of patterns in DNA sequence
plotHeatmap | Plot a Heatmap object to the device
plotHeatmap-method | Plot a Heatmap object to the device
plotHeatmapList | Plot a list of heatmaps
plotHeatmapMeta | Plot a Meta-region plot from heatmaps
plotPatternDensityMap | Plot heatmaps for several patterns in DNA sequence
plotPatternDensityMap-method | Plot heatmaps for several patterns in DNA sequence
plot_clusters | Plot partition in a separate panel
plot_legend | Plot a color legend for a heatmap
PWMScanHeatmap | Generate a Heatmap of PWM Scores in DNA sequnce
PWMScanHeatmap-method | Generate a Heatmap of PWM Scores in DNA sequnce
rev-method | Reflect a heatmap in the x axis
rle_list | Data for man page examples
scale | Return or set the scale in a Heatmap
scale-method | Return or set the scale in a Heatmap
scale<- | Return or set the scale in a Heatmap
scale<--method | Return or set the scale in a Heatmap
smoothHeatmap | Smooth a heatmap
smoothHeatmap-method | Smooth a heatmap
string_set | Data for man page examples
tata_pwm | Data for man page examples
width-method | Return the width of sequence represented in a heatmap
windows | Data for man page examples
xm | Generate co-ordinates for each row of the image matrix of a Heatmap
xm-method | Generate co-ordinates for each row of the image matrix of a Heatmap
ym | Generate co-ordinates for each column of the image matrix of a Heatmap
ym-method | Generate co-ordinates for each column of the image matrix of a Heatmap