Flexible Heatmaps for Functional Genomics and Sequence Features


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Documentation for package ‘heatmaps’ version 1.10.0

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