Quick Manual for iGenomicViewer (R code)
目录
1 Introduction 3
2 Band, Mapping, and Annotation Information 5
2.1 Band Information Object . . . . . . . . . . . . . . . . . . . . . . 5
2.2 Mapping Object . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.3 Annotation Object . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3 Initializing Objects 12
3.1 initGGV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.1.1 specifiying the heatmap matrix, mapping object, and annotation
object . . . . . . . . . . . . . . . . . . . . . . . . 12
3.1.2 specifying the tool-tip content and incorporating hyperlinks 14
3.1.3 specifying chromosome arms and known regions of interest 15
3.1.4 adding an additional [statistical] genomic plot . . . . . . . 16
3.1.5 controlling plotting features . . . . . . . . . . . . . . . . . 17
3.1.6 controlling annotation plotting . . . . . . . . . . . . . . . 18
3.1.7 returning and saving object . . . . . . . . . . . . . . . . . 18
3.1.8 summary of code used to generate ’GGVobj’ . . . . . . . 18
3.2 initTile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.2.1 specifying heatmap matrix, mapping object, and tiling . . 19
3.2.2 controlling and subsetting data . . . . . . . . . . . . . . . 20
3.2.3 controlling axis labels and size . . . . . . . . . . . . . . . 20
3.2.4 returning and saving object . . . . . . . . . . . . . . . . . 22
3.2.5 summary code used to generate ’TIplot’ . . . . . . . . . . 22
3.3 Skipping object initialization . . . . . . . . . . . . . . . . . . . . 22
1
4 Making Plots 22
4.1 MakeGGV: plot a ’GGVobj’ object . . . . . . . . . . . . . . . . . 22
4.1.1 specifying objects, spot index and sample index . . . . . . 23
4.1.2 tiled heatmap options . . . . . . . . . . . . . . . . . . . . 25
4.1.3 plotting options . . . . . . . . . . . . . . . . . . . . . . . . 26
4.1.4 updating plots and directories . . . . . . . . . . . . . . . . 27
4.1.5 summary of code for makeGGV . . . . . . . . . . . . . . . 27
4.2 iGGVtiled: plot a ’TIplot’ object . . . . . . . . . . . . . . . . . . 33
4.2.1 specifying objects . . . . . . . . . . . . . . . . . . . . . . . 33
4.2.2 specifying tool-tip content and incorporating hyperlinks . 33
4.2.3 controlling plotting features . . . . . . . . . . . . . . . . . 33
4.2.4 adding an additional [statistical] genomic plot . . . . . . . 34
4.2.5 controlling annotation plotting . . . . . . . . . . . . . . . 34
4.2.6 plotting and output options . . . . . . . . . . . . . . . . . 34
4.2.7 summary code for iGGVtiled . . . . . . . . . . . . . . . . 35
4.3 iGGV: no object needed . . . . . . . . . . . . . . . . . . . . . . . 38
4.3.1 specifiying the heatmap matrix, mapping object, and annotation
object . . . . . . . . . . . . . . . . . . . . . . . . 38
4.3.2 specifiying the tool-tip content and incorporating hyperlinks 38
4.3.3 subsetting data . . . . . . . . . . . . . . . . . . . . . . . . 38
4.3.4 plotting options . . . . . . . . . . . . . . . . . . . . . . . . 39
4.3.5 adding an additional [statistical] genomic plot . . . . . . . 41
4.3.6 controlling annotation plotting . . . . . . . . . . . . . . . 41
4.3.7 plotting and output options . . . . . . . . . . . . . . . . . 41
4.3.8 summary of code for iGGV . . . . . . . . . . . . . . . . . 42
4.4 makeTiled: a static plot . . . . . . . . . . . . . . . . . . . . . . . 42
5 Examples 44
5.1 1: aCGH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.2 2: SNPchip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.3 3: package example of plotting GGVobj . . . . . . . . . . . . . . 47
5.4 4: package example of Tiled Plot . . . . . . . . . . . . . . . . . . 48
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发表于 2013-2-14 23:28:56