代表基因组间隔数据。需要一些帮助
我正在尝试获取基因组数据的特定表示。我的数据包含在不同染色体中具有特定起始和终止位置的片段。在下表中，您将找到三列：第一列是染色体的编号，第二列是感兴趣的段（pos1）的起始位置，然后是感兴趣的段（pos2）的结束位置：
Chr pos1 pos2
1 12900000 13700000
1 21200000 21500000
1 45300000 45700000
1 45900000 46600000
1 49400000 50600000
1 51000000 52000000
1 52500000 53000000
1 73400000 74100000
1 92700000 93400000
1 114100000 114400000
1 115400000 115500000
1 145700000 146500000
1 155200000 155900000
1 173500000 175000000
1 186400000 186700000
2 24100000 24500000
2 32000000 32400000
2 61500000 61800000
2 63000000 64300000
2 72500000 73100000
2 78700000 78700000
2 81800000 82200000
2 87000000 88300000
2 95600000 97100000
2 97800000 98300000
2 99700000 100100000
2 110600000 111400000
2 135900000 136500000
2 148600000 148900000
2 155900000 156400000
2 162400000 162600000
2 176300000 176400000
2 186400000 187500000
2 189200000 189700000
2 190000000 190300000
2 193800000 195000000
2 197600000 197600000
2 200900000 201200000
2 203800000 204400000
2 214300000 214600000
3 17400000 17800000
3 44400000 44800000
3 47100000 48500000
3 48800000 51800000
3 52600000 52800000
3 57500000 57800000
3 80700000 81000000
3 83200000 83400000
3 85500000 86000000
3 89600000 90400000
3 99500000 100000000
3 101100000 101400000
3 120700000 121200000
3 135900000 136700000
3 158000000 158300000
3 162500000 163200000
3 163400000 164200000
3 180700000 181000000
4 19200000 19800000
4 33800000 34300000
4 46700000 46700000
4 48400000 49000000
4 52800000 53200000
4 64700000 65000000
4 69400000 69900000
4 74200000 74300000
4 97100000 97400000
4 98600000 99000000
4 103800000 103900000
4 107000000 107500000
4 119100000 119600000
4 120300000 120600000
4 123200000 123500000
4 127800000 128100000
4 128700000 129200000
4 144800000 145000000
4 145800000 146000000
4 151400000 152000000
4 219200000 219800000
4 233800000 234300000
4 246700000 246700000
4 248400000 249000000
5 15500000 15500000
5 36900000 37700000
5 41800000 42200000
5 43500000 44200000
5 44600000 46300000
5 49600000 50100000
5 60000000 60400000
5 63400000 63700000
5 86600000 87000000
5 87200000 87900000
5 93100000 93500000
5 130000000 131300000
5 137200000 137600000
6 26500000 27100000
6 27500000 28500000
6 32800000 33500000
6 34800000 34900000
6 44800000 45300000
6 49000000 49300000
6 62100000 63800000
6 64300000 64600000
6 69900000 70100000
6 75000000 75000000
6 76200000 76600000
6 86300000 86900000
6 115400000 115900000
6 126700000 127100000
6 140500000 140700000
6 140900000 141000000
6 145900000 146600000
7 55900000 56700000
7 56900000 57200000
7 64400000 66400000
7 69100000 69900000
7 84300000 84500000
7 91400000 92000000
7 99800000 100200000
7 102300000 103000000
7 110900000 111200000
7 117900000 118300000
7 124600000 124800000
7 133200000 133600000
8 36100000 36400000
8 42800000 43700000
8 47100000 49000000
8 50200000 50800000
8 51200000 51300000
8 67600000 68200000
8 71600000 72000000
8 76700000 77000000
8 86600000 86900000
8 99600000 100800000
8 104600000 105000000
8 111500000 111800000
8 113000000 113300000
8 114000000 114500000
9 11400000 11800000
9 15700000 15900000
9 30400000 30900000
9 33800000 34200000
9 84600000 85100000
9 95100000 95600000
9 97600000 98100000
9 99400000 100000000
9 102400000 103200000
9 123900000 124200000
9 125700000 126000000
9 126400000 126600000
9 127700000 128700000
9 129800000 130100000
10 11400000 11800000
10 15700000 15900000
10 30400000 30900000
10 33800000 34200000
10 84600000 85100000
10 95100000 95600000
10 97600000 98100000
10 99400000 100000000
10 102400000 103200000
10 123900000 124200000
10 125700000 126000000
10 126400000 126600000
10 127700000 128700000
10 129800000 130100000
11 10000000 10300000
11 14500000 14900000
11 28000000 28500000
11 31200000 31800000
11 38600000 38600000
11 38800000 39000000
11 46500000 51500000
11 54900000 56400000
11 57600000 57900000
11 66300000 66600000
11 71500000 71800000
11 84800000 85500000
11 89500000 89900000
11 111600000 111900000
12 33800000 34800000
12 38100000 39200000
12 39800000 40000000
12 46800000 47100000
12 74200000 74600000
12 82700000 83100000
12 85700000 86000000
12 86400000 87700000
12 88800000 88800000
12 110400000 111200000
12 112000000 112900000
12 123400000 123900000
13 20100000 20100000
13 35600000 35900000
13 52700000 53300000
13 55800000 58600000
13 60400000 60700000
13 65600000 65900000
13 81300000 81300000
13 83600000 83700000
13 87100000 87900000
13 89300000 90000000
13 96500000 96800000
14 37600000 38000000
14 45400000 46000000
14 60400000 61500000
14 66800000 67800000
14 68400000 68700000
14 89000000 89300000
15 28700000 29200000
15 43000000 44200000
15 49400000 50000000
15 57200000 57300000
15 64500000 65100000
15 72200000 72900000
15 77500000 77800000
15 82600000 83400000
16 14600000 15500000
16 18300000 18800000
16 32000000 35000000
16 66900000 68400000
16 69100000 69300000
16 71600000 72200000
17 18400000 18600000
17 19900000 20600000
17 28100000 28500000
17 44200000 44800000
17 58900000 59000000
18 18700000 19400000
18 26200000 26600000
18 46700000 47000000
18 50700000 50900000
19 21300000 21700000
19 37200000 38400000
19 42700000 43800000
20 25300000 26200000
20 32600000 33800000
20 34000000 34800000
22 28400000 29100000
22 30100000 30600000
22 40700000 41700000
我的目的是将这些数据表示在如下图中：
我需要的是在黑色线上用红色表示pos1和pos2之间的线段，表示Chr的总延伸。每个Chr的长度如下：
chr long
[1,] 1 250000000
[2,] 2 250000000
[3,] 3 200000000
[4,] 4 200000000
[5,] 5 182000000
[6,] 6 171000000
[7,] 7 160000000
[8,] 8 146000000
[9,] 9 139000000
[10,] 10 133900000
[11,] 11 136000000
[12,] 12 134000000
[13,] 13 115000000
[14,] 14 108000000
[15,] 15 102000000
[16,] 16 91000000
[17,] 17 84000000
[18,] 18 81000000
[19,] 19 59000000
[20,] 20 64000000
[21,] 21 49000000
[22,] 22 52000000
我希望能够像上面的图像一样创建一个图形，但能够略微改变它，例如，如果我只想表示许多不同种群的Chr1而不是特定种群的所有Chr。
我真的希望你能帮助我，因为我真的不知道如何开始。谢谢。
1 个答案:
答案 0 :(得分：0)
您可以使用geom_segment中的ggplot2为染色体长度绘制黑线（使用d_chr数据），然后使用pos1和pos2之间的较粗（lwd = 3）红色段细分（d）数据：
注意4号染色体上您的片段和染色体长度的问题。
以下是制作情节的代码：
library(ggplot2)
d <- structure(list(Chr = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L,
14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 16L,
16L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 17L, 18L, 18L, 18L,
18L, 19L, 19L, 19L, 20L, 20L, 20L, 22L, 22L, 22L), pos1 = c(12900000L,
21200000L, 45300000L, 45900000L, 49400000L, 51000000L, 52500000L,
73400000L, 92700000L, 114100000L, 115400000L, 145700000L, 155200000L,
173500000L, 186400000L, 24100000L, 32000000L, 61500000L, 63000000L,
72500000L, 78700000L, 81800000L, 87000000L, 95600000L, 97800000L,
99700000L, 110600000L, 135900000L, 148600000L, 155900000L, 162400000L,
176300000L, 186400000L, 189200000L, 190000000L, 193800000L, 197600000L,
200900000L, 203800000L, 214300000L, 17400000L, 44400000L, 47100000L,
48800000L, 52600000L, 57500000L, 80700000L, 83200000L, 85500000L,
89600000L, 99500000L, 101100000L, 120700000L, 135900000L, 158000000L,
162500000L, 163400000L, 180700000L, 19200000L, 33800000L, 46700000L,
48400000L, 52800000L, 64700000L, 69400000L, 74200000L, 97100000L,
98600000L, 103800000L, 107000000L, 119100000L, 120300000L, 123200000L,
127800000L, 128700000L, 144800000L, 145800000L, 151400000L, 219200000L,
233800000L, 246700000L, 248400000L, 15500000L, 36900000L, 41800000L,
43500000L, 44600000L, 49600000L, 60000000L, 63400000L, 86600000L,
87200000L, 93100000L, 130000000L, 137200000L, 26500000L, 27500000L,
32800000L, 34800000L, 44800000L, 49000000L, 62100000L, 64300000L,
69900000L, 75000000L, 76200000L, 86300000L, 115400000L, 126700000L,
140500000L, 140900000L, 145900000L, 55900000L, 56900000L, 64400000L,
69100000L, 84300000L, 91400000L, 99800000L, 102300000L, 110900000L,
117900000L, 124600000L, 133200000L, 36100000L, 42800000L, 47100000L,
50200000L, 51200000L, 67600000L, 71600000L, 76700000L, 86600000L,
99600000L, 104600000L, 111500000L, 113000000L, 114000000L, 11400000L,
15700000L, 30400000L, 33800000L, 84600000L, 95100000L, 97600000L,
99400000L, 102400000L, 123900000L, 125700000L, 126400000L, 127700000L,
129800000L, 11400000L, 15700000L, 30400000L, 33800000L, 84600000L,
95100000L, 97600000L, 99400000L, 102400000L, 123900000L, 125700000L,
126400000L, 127700000L, 129800000L, 10000000L, 14500000L, 28000000L,
31200000L, 38600000L, 38800000L, 46500000L, 54900000L, 57600000L,
66300000L, 71500000L, 84800000L, 89500000L, 111600000L, 33800000L,
38100000L, 39800000L, 46800000L, 74200000L, 82700000L, 85700000L,
86400000L, 88800000L, 110400000L, 112000000L, 123400000L, 20100000L,
35600000L, 52700000L, 55800000L, 60400000L, 65600000L, 81300000L,
83600000L, 87100000L, 89300000L, 96500000L, 37600000L, 45400000L,
60400000L, 66800000L, 68400000L, 89000000L, 28700000L, 43000000L,
49400000L, 57200000L, 64500000L, 72200000L, 77500000L, 82600000L,
14600000L, 18300000L, 32000000L, 66900000L, 69100000L, 71600000L,
18400000L, 19900000L, 28100000L, 44200000L, 58900000L, 18700000L,
26200000L, 46700000L, 50700000L, 21300000L, 37200000L, 42700000L,
25300000L, 32600000L, 34000000L, 28400000L, 30100000L, 40700000L
), pos2 = c(13700000L, 21500000L, 45700000L, 46600000L, 50600000L,
52000000L, 53000000L, 74100000L, 93400000L, 114400000L, 115500000L,
146500000L, 155900000L, 175000000L, 186700000L, 24500000L, 32400000L,
61800000L, 64300000L, 73100000L, 78700000L, 82200000L, 88300000L,
97100000L, 98300000L, 100100000L, 111400000L, 136500000L, 148900000L,
156400000L, 162600000L, 176400000L, 187500000L, 189700000L, 190300000L,
195000000L, 197600000L, 201200000L, 204400000L, 214600000L, 17800000L,
44800000L, 48500000L, 51800000L, 52800000L, 57800000L, 81000000L,
83400000L, 86000000L, 90400000L, 100000000L, 101400000L, 121200000L,
136700000L, 158300000L, 163200000L, 164200000L, 181000000L, 19800000L,
34300000L, 46700000L, 49000000L, 53200000L, 65000000L, 69900000L,
74300000L, 97400000L, 99000000L, 103900000L, 107500000L, 119600000L,
120600000L, 123500000L, 128100000L, 129200000L, 145000000L, 146000000L,
152000000L, 219800000L, 234300000L, 246700000L, 249000000L, 15500000L,
37700000L, 42200000L, 44200000L, 46300000L, 50100000L, 60400000L,
63700000L, 87000000L, 87900000L, 93500000L, 131300000L, 137600000L,
27100000L, 28500000L, 33500000L, 34900000L, 45300000L, 49300000L,
63800000L, 64600000L, 70100000L, 75000000L, 76600000L, 86900000L,
115900000L, 127100000L, 140700000L, 141000000L, 146600000L, 56700000L,
57200000L, 66400000L, 69900000L, 84500000L, 92000000L, 100200000L,
103000000L, 111200000L, 118300000L, 124800000L, 133600000L, 36400000L,
43700000L, 49000000L, 50800000L, 51300000L, 68200000L, 72000000L,
77000000L, 86900000L, 100800000L, 105000000L, 111800000L, 113300000L,
114500000L, 11800000L, 15900000L, 30900000L, 34200000L, 85100000L,
95600000L, 98100000L, 100000000L, 103200000L, 124200000L, 126000000L,
126600000L, 128700000L, 130100000L, 11800000L, 15900000L, 30900000L,
34200000L, 85100000L, 95600000L, 98100000L, 100000000L, 103200000L,
124200000L, 126000000L, 126600000L, 128700000L, 130100000L, 10300000L,
14900000L, 28500000L, 31800000L, 38600000L, 39000000L, 51500000L,
56400000L, 57900000L, 66600000L, 71800000L, 85500000L, 89900000L,
111900000L, 34800000L, 39200000L, 40000000L, 47100000L, 74600000L,
83100000L, 86000000L, 87700000L, 88800000L, 111200000L, 112900000L,
123900000L, 20100000L, 35900000L, 53300000L, 58600000L, 60700000L,
65900000L, 81300000L, 83700000L, 87900000L, 90000000L, 96800000L,
38000000L, 46000000L, 61500000L, 67800000L, 68700000L, 89300000L,
29200000L, 44200000L, 50000000L, 57300000L, 65100000L, 72900000L,
77800000L, 83400000L, 15500000L, 18800000L, 35000000L, 68400000L,
69300000L, 72200000L, 18600000L, 20600000L, 28500000L, 44800000L,
59000000L, 19400000L, 26600000L, 47000000L, 50900000L, 21700000L,
38400000L, 43800000L, 26200000L, 33800000L, 34800000L, 29100000L,
30600000L, 41700000L)), .Names = c("Chr", "pos1", "pos2"), row.names = c(NA,
-241L), class = "data.frame")
d_chr <- structure(list(chr = 1:22, long = c(250000000L, 250000000L, 200000000L,
200000000L, 182000000L, 171000000L, 160000000L, 146000000L, 139000000L,
133900000L, 136000000L, 134000000L, 115000000L, 108000000L, 102000000L,
91000000L, 84000000L, 81000000L, 59000000L, 64000000L, 49000000L,
52000000L)), .Names = c("Chr", "long"), class = "data.frame", row.names = c(NA,
-22L))
ggplot(d) +
geom_segment(aes(y = Chr, yend = Chr, x = 0, xend = long), data = d_chr) +
geom_segment(aes(y = Chr, yend = Chr, x = pos1, xend = pos2), lwd = 3,
colour = "red") + ylab("Chromosome") + xlab("Position (bp)")
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