data.frame format

What is data.frame?

data.frame in R is a table or a two-dimensional array-like structure in which each column contains values of one variable and each row contains one set of values from each column.

The details for data.frame is available here

Why using data.frame

It is because that most of R packages are supporting this type of data structure, such as tidyverse, reshape2...
And meanwhile, data.frame can be easily transformed to other structure, such as matrix, array, list...

Data structure of each function

The data structure among each function is different, details are showing below.

CircosArc()

chr start end color des link html
EGFR 57 167 #FFBB77 Recep_L_domain NA
EGFR 185 338 #FF7F0E Furin-like_domain https://www.intogen.org/search?gene=EGFR NA
EGFR 361 480 #FFBB77 Recep_L_domain https://www.intogen.org/search?gene=EGFR NA
EGFR 505 636 #1F77B4 GF_recep_IV_domain NA
EGFR 713 965 #AEC6E7 Pkinase_Tyr_domain NA

Full example of data can be found through ?arcExample

CircosAuxLine()

No data should be input to CircosAuxLine()

CircosBackground()

No data should be input to CircosBackground()

CircosBubble()

chr start end name value layer color html
2L 1 1011544 TP53 0.8 1 NA NA
2L 1011548 2011544 TP53 0.3 1 NA NA
... ... ... ... ... ... ... ...
X 20011548 21146708 TP53 0.49 1 NA NA
X 21011548 22422827 TP53 0.83 1 NA NA

Full example of data can be found through ?bubbleExample

CircosChord()

C.CK C.NPK ... Basidiomycota Zygomycota
0 0 ... 24.75 18.49
0 0 ... 24.18 29.3
... ... ... ... ...
24.75 24.18 ... 0 0
18.49 29.3 ... 0 0

Full example of data can be found through ?chordExample

CircosChord.p()

source_chr source_start source_end target_chr target_start target_end
19 22186054 26186054 17 31478117 35478117
4 74807187 78807187 1 89852878 93852878
... ... ... ... ... ...
17 31478117 35478117 1 89852849 93852849
17 31478114 31478114 X 106297713 110297713

Full example of data can be found through ?chord.pExample

CircosCnv()

chr start end value link color html
1 764788 87109267 2.5 NA NA NA
1 87109268 120217058 2.0 NA NA NA
... ... ... ... ... ... ...
3 125251487 125456654 5 NA NA NA
3 125456655 127048011 4 NA NA NA

Full example of data can be found through ?cnvExample

CircosGene()

chr strand start end type name link html
EGFR - 1 250 gene EGFR https://www.intogen.org/search?gene=EGFR NA
EGFR - 1 30 utr EGFR https://www.intogen.org/search?gene=EGFR NA
... ... ... ... ... ... ... ...
EGFR - 920 935 cds EGFR https://www.intogen.org/search?gene=EGFR NA
EGFR - 935 950 utr EGFR https://www.intogen.org/search?gene=EGFR NA

Full example of data can be found through ?geneExample

CircosHeatmap()

chr start end name value layer html
2L 1 1011544 TP53 0.8 1 NA NA
2L 1011548 2011544 TP53 0.3 1 NA NA
... ... ... ... ... ... ... ...
X 20011548 21146708 TP53 0.49 1 NA NA
X 21011548 22422827 TP53 0.83 1 NA NA

Full example of data can be found through ?heatmapExample

CircosHistogram()

chr start end name value layer html
2L 1 1011544 TP53 0.8 1 NA NA
2L 1011548 2011544 TP53 0.3 1 NA NA
... ... ... ... ... ... ... ...
X 20011548 21146708 TP53 0.49 1 NA NA
X 21011548 22422827 TP53 0.83 1 NA NA

Full example of data can be found through ?histogramExample

CircosLegend()

No data should be input to CircosLegend()

CircosLine()

chr pos value des html
1 813468 0.15 NA NA
1 3383745 0.122385 NA NA
... ... ... ... ...
7 141390027 0.0922775 NA NA
7 146503088 0.1907651 NA NA

Full example of data can be found through ?lineExample

CircosLink()

fusion g1chr g1start g1end g1name g2chr g2start g2end g2name link html
FGFR3--TACC3 4 1795662 1808986 FGFR3 4 1723217 1746905 TACC3 NA NA
CCDC6--RET 10 43595894 43623714 RET 10 61552678 61666182 TACC3 NA NA
... ... ... ... ... ... ... ... ... ... ...
ABL1--BCR 9 133589707 133761067 ABL1 22 23523148 23657706 BCR NA NA
SND1--BRAF 7 127292043 127732659 SND1 7 140434400 140624503 BRAF NA NA

Full example of data can be found through ?linkExample

CircosLollipop()

protein chr pos strand CancerTypeNumber AA_pos AA_change Consequence color type link html
EGFR 7 101219410 + 2 AA_858 L/R missense_variant #FEFF00 Hetero NA
EGFR 7 101219417 + 2 AA_858 L/R missense_variant #FEFF00 Homo NA
EGFR 7 101219425 + 1 AA_858 L/R missense_variant #FEFF00 Homo NA
... ... ... ... ... ... ... ... ... ... ... ...

Full example of data can be found through ?lollipopExample

CircosScatter()

chr start end name des link html
12 125550131 125626772 AACS liver NA NA
9 107546599 107665960 ABCA1 colorectal NA NA
16 2326678 2376467 ABCA3 breast NA NA
... ... ... ... ... ... ...

Full example of data can be found through ?scatterExample

CircosSnp()

chr pos value des color r2value link index image html
1 813468 0.714061 GWAS_SNP NA NA NA NA NA NA
1 3383745 0.22385 GWAS_SNP NA NA NA NA NA NA
1 6157646 0.238643 GWAS_SNP NA NA NA NA NA NA
... ... ... ... ... ... ... ... ... ...

Full example of data can be found through ?snpExample

CircosText()

No data should be input to CircosText()

CircosWig()

chr pos value des html
chr8 0.024557353699565337 5 NA NA
chr8 0.5157044276908721 5 NA NA
chr8 1.0068515016821786 4 NA NA
... ... ... ... ...

Full example of data can be found through ?wigExample