Flexible Heatmaps for Functional Genomics and Sequence Features
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Documentation for package ‘heatmaps’ version 1.33.0
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 |