Circlize plot - Does not draw clear lines
I have this script, which results in this really pretty circlize plot.
install.packages('circlize', repos = "http://cran.rstudio.com/" )
install.packages('data.table', repos = "http://cran.rstudio.com/")
library(circlize)
library(data.table)
karyo <- fread(colClasses = c("character", "numeric",
"numeric", "character", "character"),
"ssa01 0 45670927 1p gneg
ssa01 45670927 102921759 1qa gpos50
ssa01 102921759 158994226 1qb gneg
ssa02 0 37194884 2p gpos50
ssa02 37194884 72887026 2q gneg
ssa03 0 53325515 3p gpos50
ssa03 53325515 92451775 3q gneg
ssa04 0 24769547 4p gpos50
ssa04 24769547 82368206 4q gneg
ssa05 0 44366638 5p gpos50
ssa05 44366638 80452451 5q gneg
ssa06 0 44681795 6p gpos50
ssa06 44681795 87037992 6q gneg
ssa07 0 29822415 7p gpos50
ssa07 29822415 58755209 7q gneg
ssa08 -15000000 0 rDNA gpos50
ssa08 0 26442203 8q gneg
ssa09 0 48560009 9qa gpos50
ssa09 48560009 92800824 9qb gneg
ssa09 92800824 141678924 9qc gpos50
ssa10 0 50712303 10qa gneg
ssa10 50712303 116119932 10qb gpos50
ssa11 0 44252459 11qa gneg
ssa11 44252459 93835980 11qb gpos50
ssa12 0 31366442 12qa gneg
ssa12 31366442 91841354 12qb gpos50
ssa13 0 46825690 13qa gneg
ssa13 46825690 107755956 13qb gpos50
ssa14 0 45561258 14qa gneg
ssa14 45561258 93876043 14qb gpos50
ssa15 0 53413608 15qa gneg
ssa15 53413608 103934464 15qb gpos50
ssa16 0 56974611 16qa gneg
ssa16 56974611 87752276 16qb gpos50
ssa17 0 31608156 17qa gneg
ssa17 31608156 57636407 17qb gpos50
ssa18 0 35154609 18qa gneg
ssa18 35154609 70656513 18qb gpos50
ssa19 0 38868197 19qa gneg
ssa19 38868197 82958981 19qb gpos50
ssa20 0 40962200 20qa gneg
ssa20 40962200 86771154 20qb gpos50
ssa21 0 58011450 21 gneg
ssa22 0 63437620 22 gneg
ssa23 0 49935705 23 gneg
ssa24 0 48640078 24 gneg
ssa25 0 51465665 25 gneg
ssa26 0 47887414 26 gneg
ssa27 0 43932925 27 gneg
ssa28 0 39590257 28 gneg
ssa29 0 42472244 29 gneg")
cells <- fread("ssa01 0 6843616 ssa09 48497608 43657580 cigene_21_21
ssa01 6946687 8594997 ssa09 4749099 6657810 cigene_21_21
ssa01 8761342 9088168 ssa09 270912 155778 cigene_21_21
ssa01 9158929 44448014 ssa09 6779314 43613554 cigene_21_21
ssa01 44464323 45490398 ssa09 4717661 3644783 cigene_21_21
ssa01 45851456 71976385 ssa18 2845971 28112522 cigene_21_21
ssa01 72879911 73557255 ssa28 34194749 34694334 cigene_21_21
ssa01 73558102 88357101 ssa28 13189995 24991882 cigene_21_21
ssa01 88393814 90591948 ssa18 28120583 30993608 cigene_21_21
ssa01 90719401 99584790 ssa28 25023445 33200917 cigene_21_21
ssa01 106258728 106674403 ssa13 101000184 100406704 cigene_21_21
ssa01 108338976 115563273 ssa13 98799652 90773398 cigene_21_21
ssa01 116910054 121177528 ssa13 90772566 85845771 cigene_21_21
ssa01 121201942 142747918 ssa11 72697822 49568288 cigene_21_21
ssa01 144877136 145895090 ssa11 45581503 44384062 cigene_21_21
ssa01 146151174 149925087 ssa11 46202668 49405861 cigene_21_21
ssa01 153001283 156331869 ssa13 101054432 107355605 cigene_21_21
ssa01 156444877 158990959 ssa13 107565689 103272042 cigene_21_21
ssa02 0 37183267 ssa05 80452451 44387533 cigene_21_3
ssa02 37206501 72887026 ssa12 31357447 0 cigene_21_3
ssa03 364935 2747440 ssa14 47030385 45149425 cigene_21_5
ssa03 1122363 4195588 ssa14 50783037 48525974 cigene_21_5
ssa03 5212593 44547960 ssa14 4919797 44703263 cigene_21_5
ssa03 44841249 47252771 ssa13 16080251 13167425 cigene_21_5
ssa03 47268596 48018298 ssa05 18588680 19685350 cigene_21_5
ssa03 48048600 52186527 ssa23 780875 3112448 cigene_21_5
ssa03 52649577 53313933 ssa23 0 757933 cigene_21_5
ssa03 53337097 92451775 ssa06 44497429 0 cigene_21_5
ssa04 0 15341445 ssa08 26055991 7829984 cigene_21_7
ssa04 15621004 24719742 ssa08 0 7829984 cigene_21_7
ssa04 24819351 28652971 ssa10 53060574 52329613 cigene_21_7
ssa04 29656081 31102993 ssa10 58161834 59807071 cigene_21_7
ssa04 31198629 38035923 ssa11 84682864 75019162 cigene_21_7
ssa04 38138247 39124546 ssa11 74095227 72787793 cigene_21_7
ssa04 39186468 77325076 ssa13 85759651 46939698 cigene_21_7
ssa04 77398345 77760129 ssa10 60384152 59876005 cigene_21_7
ssa04 77892210 82302510 ssa11 84885734 93658279 cigene_21_7
ssa05 0 16783642 ssa09 91697818 76066628 cigene_21_8
ssa05 19797082 44345743 ssa09 48622409 74756512 cigene_21_8
ssa06 44866160 63240934 ssa15 20326123 38376064 cigene_21_9
ssa06 63349385 64012747 ssa15 50808339 50100071 cigene_21_9
ssa06 64037873 79441812 ssa15 54460690 41235676 cigene_21_9
ssa06 79475283 86773188 ssa15 20195818 10834079 cigene_21_9
ssa07 0 3169069 ssa18 70509147 67091998 cigene_21_10
ssa07 4717043 12776862 ssa18 39315610 48836242 cigene_21_10
ssa07 12782626 13557017 ssa18 49636752 48855526 cigene_21_10
ssa07 13559138 29545108 ssa18 49668386 66913352 cigene_21_10
ssa07 30099722 58321216 ssa17 31965773 57540086 cigene_21_10
ssa09 372600 2523774 ssa11 4568887 112654 cigene_21_11
ssa09 91740478 92636663 ssa20 1005209 0 cigene_21_11
ssa09 92964984 138116665 ssa20 40968350 80791454 cigene_21_11
ssa10 6516854 9083984 ssa16 55080990 51872091 cigene_21_12
ssa10 9912722 19185602 ssa16 49756067 37311992 cigene_21_12
ssa10 19292640 49094993 ssa23 33285371 3126275 cigene_21_12
ssa10 64886930 73893160 ssa23 43112254 33350463 cigene_21_12
ssa10 73919063 111715556 ssa16 37287700 0 cigene_21_12
ssa10 111895177 116088268 ssa23 43217075 48795685 cigene_21_12
ssa11 4847201 10220648 ssa26 4517045 10259102 cigene_21_13
ssa11 10245832 14795494 ssa26 15137018 10259113 cigene_21_13
ssa11 14804709 44120855 ssa26 15138210 47884620 cigene_21_13
ssa12 31375436 35524288 ssa22 4152549 0 cigene_21_14
ssa12 35542504 83373635 ssa22 51996806 4158499 cigene_21_14
ssa12 83746172 91723600 ssa22 52043634 63200112 cigene_21_14
ssa13 0 7174925 ssa15 103591384 95503623 cigene_21_15
ssa13 7175841 10333631 ssa15 70707775 73414810 cigene_21_15
ssa13 16120805 22268064 ssa15 56018876 62832409 cigene_21_15
ssa13 22331525 26381128 ssa15 79477647 75176327 cigene_21_15
ssa13 26404080 28835918 ssa15 65671872 63102592 cigene_21_15
ssa13 28929493 31820350 ssa15 68453835 66050303 cigene_21_15
ssa13 31824704 43526833 ssa15 94392728 79480752 cigene_21_15
ssa13 43530010 44484971 ssa15 95236934 95503623 cigene_21_15
ssa13 44567360 46711682 ssa15 70671711 68607378 cigene_21_15
ssa14 47114391 48433466 ssa27 5232718 3582537 cigene_21_17
ssa14 51604585 54683245 ssa27 0 3582218 cigene_21_17
ssa14 54767228 71598820 ssa27 5665886 22486246 cigene_21_17
ssa14 71685703 85987446 ssa27 36363992 22551628 cigene_21_17
ssa14 86001684 93798132 ssa27 36387980 43151030 cigene_21_17
ssa15 0 1777952 ssa24 1793564 468390 cigene_21_18
ssa15 2568097 10380129 ssa24 40547260 47817636 cigene_21_18
ssa16 58868231 87752276 ssa17 1168292 31250539 cigene_21_2
ssa18 514148 2792680 ssa19 66054142 63968520 cigene_21_1
ssa19 0 4398723 ssa19 55763317 51509249 cigene_21_4
ssa19 8209966 14853065 ssa29 27579285 36466443 cigene_21_4
ssa19 16742039 32839049 ssa29 0 16247061 cigene_21_4
ssa19 32865538 38853352 ssa28 39589923 34718551 cigene_21_4
ssa19 38883042 51480644 ssa28 13108997 0 cigene_21_4
ssa19 60868480 61508995 ssa28 7219775 7725975 cigene_21_4
ssa19 62735943 63378768 ssa19 4901716 7586712 cigene_21_4
ssa19 66256876 78280992 ssa29 27576310 16856802 cigene_21_4
ssa19 78320578 82952330 ssa29 36474059 42376689 cigene_21_4
ssa20 1080524 4216238 ssa24 4661034 1836998 cigene_21_6
ssa20 5246663 29618716 ssa24 40253535 14198356 cigene_21_6
ssa20 29625403 30290372 ssa24 13580940 14165236 cigene_21_6
ssa20 30290972 40956049 ssa24 13547900 4663342 cigene_21_6
ssa21 0 5534565 ssa25 4156252 0 grey
ssa21 5593276 17047359 ssa25 4658816 14846060 grey
ssa21 17069345 51519898 ssa25 47016726 14853562 grey
ssa21 51921340 58011450 ssa25 47405282 51465665 grey")
names(cells) <- c("chr1", "start1", "end1", "chr2", "start2", "end2", "col")
cells <- data.frame(cells)
regions_annot <- fread("ssa01 0 10000000 ssa01 region_telomeric
ssa01 10000000 148994226 ssa01 region_normal
ssa01 148994226 158994226 ssa01 region_telomeric
ssa02 0 12000000 ssa02 region_collapsed
ssa02 12000001 51206500 ssa02 region_highid
ssa02 51206500 72887026 ssa02 region_collapsed
ssa03 0 10000000 ssa03 region_telomeric
ssa03 10000000 50048600 ssa03 region_normal
ssa03 50048600 69337097 ssa03 region_highid
ssa03 69337097 92451775 ssa03 region_collapsed
ssa04 0 11000000 ssa04 region_collapsed
ssa04 11000001 25621004 ssa04 region_highid
ssa04 25621004 72368206 ssa04 region_normal
ssa04 72368206 82368206 ssa04 region_telomeric
ssa05 0 8000000 ssa05 region_highid
ssa05 8000000 43452452 ssa05 region_normal
ssa05 43452452 69452452 ssa05 region_highid
ssa05 69452452 80452451 ssa05 region_collapsed
ssa06 0 27497429 ssa06 region_collapsed
ssa06 27497429 44866161 ssa06 region_highid
ssa06 44866161 77037992 ssa06 region_normal
ssa06 77037992 87037992 ssa06 region_telomeric
ssa07 0 10000000 ssa07 region_telomeric
ssa07 10000000 31099723 ssa07 region_normal
ssa07 31099723 47099723 ssa07 region_highid
ssa07 47099723 58755209 ssa07 region_collapsed
ssa08 0 16055992 ssa08 region_highid
ssa08 16055992 26442203 ssa08 region_collapsed
ssa09 0 84697819 ssa09 region_normal
ssa09 84697819 141678924 ssa09 region_highid
ssa10 0 106119932 ssa10 region_normal
ssa10 106119932 116119932 ssa10 region_telomeric
ssa11 0 6847202 ssa11 region_normal
ssa11 6847202 28804710 ssa11 region_highid
ssa11 28804710 44804709 ssa11 region_collapsed
ssa11 44804709 83835980 ssa11 region_normal
ssa11 83835980 93835980 ssa11 region_telomeric
ssa12 0 16357447 ssa12 region_collapsed
ssa12 16357447 30357447 ssa12 region_highid
ssa12 30357447 81841354 ssa12 region_normal
ssa12 81841354 91841354 ssa12 region_telomeric
ssa13 0 97755956 ssa13 region_normal
ssa13 97755956 107755956 ssa13 region_telomeric
ssa14 0 83876043 ssa14 region_normal
ssa14 83876043 93876043 ssa14 region_telomeric
ssa15 0 93934464 ssa15 region_normal
ssa15 93934464 103934464 ssa15 region_telomeric
ssa16 0 58868232 ssa16 region_normal
ssa16 58868232 73868231 ssa16 region_highid
ssa16 73868231 87752276 ssa16 region_collapsed
ssa17 0 16168292 ssa17 region_highid
ssa17 16168292 24168292 ssa17 region_collapsed
ssa17 24168293 48965773 ssa17 region_highid
ssa17 48965773 57636407 ssa17 region_collapsed
ssa18 0 60656513 ssa18 region_normal
ssa18 60656513 70656513 ssa18 region_telomeric
ssa19 0 72958981 ssa19 region_normal
ssa19 72958981 82958981 ssa19 region_telomeric
ssa20 0 40968350 ssa20 region_normal
ssa20 40968350 86771154 ssa20 region_highid
ssa21 0 48011450 ssa21 region_normal
ssa21 48011450 58011450 ssa21 region_telomeric
ssa22 0 53437620 ssa22 region_normal
ssa22 53437620 63437620 ssa22 region_telomeric
ssa23 0 39935705 ssa23 region_normal
ssa23 39935705 49935705 ssa23 region_telomeric
ssa24 0 38640078 ssa24 region_normal
ssa24 38640078 48640078 ssa24 region_telomeric
ssa25 0 41465665 ssa25 region_normal
ssa25 41465665 51465665 ssa25 region_telomeric
ssa26 0 6517046 ssa26 region_normal
ssa26 6517046 29138210 ssa26 region_highid
ssa26 29138210 47887414 ssa26 region_collapsed
ssa27 0 33932925 ssa27 region_normal
ssa27 33932925 43932925 ssa27 region_telomeric
ssa28 0 29590257 ssa28 region_normal
ssa28 29590257 39590257 ssa28 region_telomeric
ssa29 0 32472244 ssa29 region_normal
ssa29 32472244 42472244 ssa29 region_telomeric")
names(regions_annot) <- c("chr", "start", "end", "value", "col")
getCol <- function(r, g, b, alpha=0.8) {
rgb(r/255, g/255, b/255, alpha=alpha)
}
getColName <- function(col.in, alpha=0.8) {
co = as.numeric(col2rgb(col.in))
rgb(red=co[1]/255, green=co[2]/255, blue=co[3]/255, alpha=alpha)
}
getColFromList <- function(color) {
if (!is.function(get(color))) { return(getColName(color)) } # "grey", "black"
else { return(getColName(color)) } #cigene_21_1"
}
alpha <- 0.8
cigene_21_1 <- getCol(119,17,85,alpha)
cigene_21_2 <- getCol(170,68,136,alpha)
cigene_21_3 <- getCol(204,153,187,alpha)
cigene_21_4 <- getCol(17,68,119,alpha)
cigene_21_5 <- getCol(68,119,170,alpha)
cigene_21_6 <- getCol(119,170,221,alpha)
cigene_21_7 <- getCol(17,119,119,alpha)
cigene_21_8 <- getCol(68,170,170,alpha)
cigene_21_9 <- getCol(119,204,204,alpha)
cigene_21_10 <- getCol(17,119,68,alpha)
cigene_21_11 <- getCol(68,170,119,alpha)
cigene_21_12 <- getCol(136,204,170,alpha)
cigene_21_13 <- getCol(119,119,17,alpha)
cigene_21_14 <- getCol(170,170,68,alpha)
cigene_21_15 <- getCol(221,221,119,alpha)
cigene_21_16 <- getCol(119,68,17,alpha)
cigene_21_17 <- getCol(170,119,68,alpha)
cigene_21_18 <- getCol(221,170,119,alpha)
cigene_21_29 <- getCol(119,17,34,alpha)
cigene_21_20 <- getCol(170,68,85,alpha)
cigene_21_21 <- getCol(221,119,136,alpha)
alpha <- 1
region_telomeric <- getCol(255,255,191,alpha)
region_normal <- getCol(102,194,165,alpha)
region_collapsed <- getCol(213,62,79,alpha)
region_highid <- getCol(244,109,67,alpha)
regions_annot.bed <- data.frame(regions_annot)[1:3]
regions_annot.bed$value1 <- rep(1, nrow(regions_annot.bed))
regions_annot.bed$value2 <- rep(0, nrow(regions_annot.bed))
regions_annot.bed$col <- as.character(unlist(mget(regions_annot$col, ifnotfound = list(function(x) getColFromList(x)))))
cells$col <- as.character(unlist(mget(cells$col, ifnotfound = list(function(x) getColFromList(x)))))
par(mar = c(1, 1, 1, 1))
circos.par(start.degree = 90)
circos.initializeWithIdeogram(data.frame(karyo), track.height=0.05, ideogram.height = 0.03, chromosome.index = sort(unique(karyo$V1)))
circos.genomicTrackPlotRegion(regions_annot.bed, track.height=0.02, panel.fun = function(region, value, ...) {
circos.genomicRect(region, value, col = value$col, border = NA, ...)
})
circos.genomicLink(cells[,1:3], cells[,4:6], col = cells$col, border = NA)
I replaced what is in the cells variable with more observations, which are in this file. However, I think due to too many observations I get this pretty crappy plot.
I want the plot drawn with the data from the file (more observations) to more resemble the one in the first image. I would like that the lines in the plot don't turn out like this, because of lines that are overlapping with each other.
Does anyone have any suggestions on this?
Solution
The reason is the width of each link is too small compared to the width of contigs (or chromosomes), which makes the link too thin. Links are actually drawn as polygons and a polygon has a border and filled area. Borders are lines with certain line width in R. In some graphic device (like png), when you set border = NA to remove the borders, the remaining filled area can be even thinner and can be broken and that is why you see there are so many segments.
To solve this problem, you can do either:
- set the end positions to be the same as the start positions so that each link is plotted as lines while not polygons
- set
border = cells$colto keep the borders.
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