I am able to follow the Circlize example in the description of the package on CRAN easily:
library('circlize')
set.seed(123)
mat = matrix(sample(1:100, 18, replace = TRUE), 3, 6)
rownames(mat) = letters[1:3]
colnames(mat) = LETTERS[1:6]
### basic settings
par(mfrow = c(3, 2))
par(mar = c(1, 1, 1, 1))
chordDiagram(mat)
however, when I replace mat with myMatrix I get this error:
Error in circos.initialize(factors = factor(cate, levels = cate), xlim = cbind(rep(0, :
Since `xlim` is a matrix, it should have same number of rows as the length of the level of `factors` and number of columns of 2.
Can somebody explain why I am getting that message? I do not see a difference between mat and myMatrix other than myMatrix is larger:
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z A2 B2 C2 D2
A 1060360.659 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
B 0 32143148.75 996976.8445 0 4944648.524 5688385.041 61990.5913 0 0 0 0 -1563.225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31922242.6
C 0 0 6342776.843 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
D 0 0 0 28617385.81 17842142.64 0 0 0 0 0 0 0 0 409444.5633 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 4990921.202 105686446.3 536246.2188 0 0 0 0 0 0 0 8587899.583 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 378565.5746
F 0 92732.7741 0 4282.9319 33543553.89 36773976.59 1894761.93 0 0 333209.342 0 20739.0655 327956.7365 0 1022673.163 12229.0255 0 0 386112.1743 224039.3207 0 2395066.197 268247.2897 0 0 0 0 0 0 11926701.96
G 0 0 0 0 0 0 7753767.003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H 0 0 0 0 0 5184133.29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
I 0 0 0 0 462767.7374 0 0 0 8992223.296 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
J 0 0 0 0 0 0 0 0 0 1950552.642 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
K 0 0 0 0 891032.5584 0 0 0 0 0 520107.9821 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26724.8402 0 0 0 418902.5203
L 0 0 0 0 32044317.54 28147.5693 0 0 0 0 0 5383919.293 0 489912.5412 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4559115.003
M 0 0 0 0 0 3125823.41 0 0 0 0 0 0 1738293.164 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N 0 1053825.966 -8526.9758 1283429.314 60333051.34 2621812.931 -1130.1924 0 -779545.8004 8055145.684 918.8702 -379747.1919 -177.6205 298563606.5 -9316.8654 0 0 0 0 0 2631991.077 0 0 0 0 0 1107369.803 0 0 118812465
O 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500451.292 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7432418.396
P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Q 0 0 1496058.76 0 -4056617.74 294503 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 410.4 0 0 0 0 0 0 0 1765984767
Code
dd <- read.table(header = TRUE, text = " rn A B C D E F G H I J K L M N O P Q R S T U V W X Y Z A2 B2 C2 D2
A 1060360.659 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
B 0 32143148.75 996976.8445 0 4944648.524 5688385.041 61990.5913 0 0 0 0 -1563.225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31922242.6
C 0 0 6342776.843 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
D 0 0 0 28617385.81 17842142.64 0 0 0 0 0 0 0 0 409444.5633 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 4990921.202 105686446.3 536246.2188 0 0 0 0 0 0 0 8587899.583 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 378565.5746
F 0 92732.7741 0 4282.9319 33543553.89 36773976.59 1894761.93 0 0 333209.342 0 20739.0655 327956.7365 0 1022673.163 12229.0255 0 0 386112.1743 224039.3207 0 2395066.197 268247.2897 0 0 0 0 0 0 11926701.96
G 0 0 0 0 0 0 7753767.003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H 0 0 0 0 0 5184133.29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
I 0 0 0 0 462767.7374 0 0 0 8992223.296 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
J 0 0 0 0 0 0 0 0 0 1950552.642 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
K 0 0 0 0 891032.5584 0 0 0 0 0 520107.9821 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26724.8402 0 0 0 418902.5203
L 0 0 0 0 32044317.54 28147.5693 0 0 0 0 0 5383919.293 0 489912.5412 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4559115.003
M 0 0 0 0 0 3125823.41 0 0 0 0 0 0 1738293.164 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N 0 1053825.966 -8526.9758 1283429.314 60333051.34 2621812.931 -1130.1924 0 -779545.8004 8055145.684 918.8702 -379747.1919 -177.6205 298563606.5 -9316.8654 0 0 0 0 0 2631991.077 0 0 0 0 0 1107369.803 0 0 118812465
O 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500451.292 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7432418.396
P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Q 0 0 1496058.76 0 -4056617.74 294503 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 410.4 0 0 0 0 0 0 0 1765984767")
myMatrix <- as.matrix(dd[, -1])
rownames(myMatrix) <- dd[, 1]
chordDiagram(myMatrix)
In the old version of circlize, the matrix must be of a matrix class instead of a data.frame, so you need to convert the data frame explicitly by:
myMatrix = as.matrix(A + B)
In circlize, a data frame is for data stored as a adjacency list (e.g the first column for group1, second column for group2, third column for the strength of the relation).
Since read.table() always returns a data.frame class, in the newer version of circlize, it is fine if the matrix represents as a data frame. When it is a data frame, the chordDiagram() will first check whether the number of columns is larger than 3 and all columns are numeric. If so, it will be converted to a matrix internally.
Related
I have downloaded some files off the internet that are single cell count matrices, and I want to convert them into dataframes in R. I have used readLines to read the text files in, but now each line of the file looks like this:
3110082J24Rik\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0
For some context, the columns in a single cell matrix file are the cells, and the rows are the genes. The numbers in the file indicate the number of times that the gene (for this line, 3110082J24Rik) appears in each cell. Anyone have any idea how I could do this? Here is some sample data:
ID W308561 W308562 W308563 W308564 W308565 W308566 W308567 W308568 W308569 W308570 W308571 W308572 W308573 W308574 W308575 W308576 W308577 W308578 W308579 W308580 W308581 W308582 W308583 W308584 W308585 W308586 W308587 W308588 W308589 W308590 W308591 W308592 W308593 W308594 W308595 W308596 W308597 W308598 W308599 W308600 W308601 W308602 W308603 W308604 W308605 W308606 W308607 W308608 W308609 W308610 W308611 W308612 W308613 W308614 W308615 W308616 W308617 W308618 W308619 W308620 W308621 W308622 W308623 W308624 W308625 W308626 W308627 W308628 W308629 W308630 W308631 W308632 W308633 W308634 W308635 W308636 W308637 W308638 W308639 W308640 W308641 W308642 W308643 W308644 W308645 W308646 W308647 W308648 W308649 W308650 W308651 W308652 W308653 W308654 W308655 W308656 W308657 W308658 W308659 W308660 W308661 W308662 W308663 W308664 W308665 W308666 W308667 W308668 W308669 W308670 W308671 W308672 W308673 W308674 W308675 W308676 W308677 W308678 W308679 W308680 W308681 W308682 W308683 W308684 W308685 W308686 W308687 W308688 W308689 W308690 W308691 W308692 W308693 W308694 W308695 W308696 W308697 W308698 W308699 W308700 W308701 W308702 W308703 W308704 W308705 W308706 W308707 W308708 W308709 W308710 W308711 W308712 W308713 W308714 W308715 W308716 W308717 W308718 W308719 W308720 W308721 W308722 W308723 W308724 W308725 W308726 W308727 W308728 W308729 W308730 W308731 W308732 W308733 W308734 W308735 W308736 W308737 W308738 W308739 W308740 W308741 W308742 W308743 W308744 W308745 W308746 W308747 W308748 W308749 W308750 W308751 W308752 W308753 W308754 W308755 W308756 W308757 W308758 W308759 W308760 W308761 W308762 W308763 W308764 W308765 W308766 W308767 W308768 W308769 W308770 W308771 W308772 W308773 W308774 W308775 W308776 W308777 W308778 W308779 W308780 W308781 W308782 W308783 W308784 W308785 W308786 W308787 W308788 W308789 W308790 W308791 W308792 W308793 W308794 W308795 W308796 W308797 W308798 W308799 W308800 W308801 W308802 W308803 W308804 W308805 W308806 W308807 W308808 W308809 W308810 W308811 W308812 W308813 W308814 W308815 W308816 W308817 W308818 W308819 W308820 W308821 W308822 W308823 W308824 W308825 W308826 W308827 W308828 W308829 W308830 W308831 W308832 W308833 W308834 W308835 W308836 W308837 W308838 W308839 W308840 W308841 W308842 W308843 W308844 W308845 W308846 W308847 W308848 W308849 W308850 W308851 W308852 W308853 W308854 W308855 W308856 W308857 W308858 W308859 W308860 W308861 W308862 W308863 W308864 W308865 W308866 W308867 W308868 W308869 W308870 W308871 W308872 W308873 W308874 W308875 W308876 W308877 W308878 W308879 W308880 W308881 W308882 W308883 W308884 W308885 W308886 W308887 W308888 W308889 W308890 W308891 W308892 W308893 W308894 W308895 W308896 W308897 W308898 W308899 W308900 W308901 W308902 W308903 W308904 W308905 W308906 W308907 W308908 W308909 W308910 W308911 W308912 W308913 W308914 W308915 W308916 W308917 W308918 W308919 W308920 W308921 W308922 W308923 W308924 W308925 W308926 W308927 W308928 W308929 W308930 W308931 W308932 W308933 W308934 W308935 W308936 W308937 W308938 W308939 W308940 W308941 W308942 W308943 W308944
0610005C13Rik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0610007C21Rik 0 3 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 1 0 1 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 2 0 0 0 0 2 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 2 0 0 0 0 0 0 1 0 0 0
0610007L01Rik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0610007P08Rik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
0610007P14Rik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0610007P22Rik 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
0610008F07Rik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
In the ideal world, each of the labels at the top that starts with "W" would be a separate column with the corresponding numbers for each gene also in that column.
I have an excel table of 15200 lines, corresponding to a tree analyzed for its structures. I have all the structures in columns (48 structures), they have been counted on every tree. for example, the tree 12607 has 3 structures CV11, 1 structure IN12 and none (0) of the rest of all the structures. Thus, the table looks like a huge table with a lot of 0 and some numbers of the occurrence of structures on the trees. The very last column is the value given to the tree, according to the structures found on it (each structure giving a number of point to the tree by its presence on it).
The question is: Are there some structures, or combination of structures, which give a high value to the tree. Of course, according to the value of each structure, we can see which one has a higher value than the others (ex: structure CV11 has a value of 15, structure IN12 has a value of 4). But what I want to know is, if we take all the trees having a higher final value than 100 (we create a new dataframe "data100"), and we compare with the trees having a final value under 100 (we create another dataframe "data0"), can we find a significant difference in the number and occurrence of structures found on these trees? Because the structure with high value is maybe only found on the trees with a value under 100; because for example, this structure does not allow other structures to be found on the same tree.
Voilà, I hope I have given enough details... If you have any idea or proposition for solving this problem.. it will be great!
Below is my script.
> data100
CV11 CV12 CV13 CV14 CV15 CV21 CV22 CV23 CV24 CV25 CV26 CV31 CV32 CV33 CV41 CV42 CV43 CV44 CV51 CV52 IN11 IN12 IN13
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
13 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
15 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
IN14 IN21 IN22 IN23 IN31 IN32 IN33 IN34 BA11 BA12 BA21 DE11 DE12 DE13 DE14 DE15 GR11 GR12 GR13 GR21 GR22 GR31 GR32
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 0 0 0 0
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 0 0
13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 0 0
14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0
15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
EP11 EP12 EP13 EP14 EP21 EP31 EP32 EP33 EP34 EP35 NE11 NE12 NE21 OT11 OT12 OT21 OT22 ecoval
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63
13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77
14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54
15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20
[ reached getOption("max.print") -- omitted 60749 rows ]
> sortdata100<-data100[order(data100[,64],decreasing=T),]
> rsortdata100<-sortdata100[sortdata100$ecoval>100,]
> rsortdata100<-na.omit(rsortdata100)#181 lignes
> rsortdata100
CV11 CV12 CV13 CV14 CV15 CV21 CV22 CV23 CV24 CV25 CV26 CV31 CV32 CV33 CV41 CV42 CV43 CV44 CV51 CV52 IN11 IN12 IN13
1291 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1083 0 4 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3919 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
14685 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
4021 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
5452 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
14686 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
4022 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
1013 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2895 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4719 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0
682 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
3444 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1299 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
2713 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0
IN14 IN21 IN22 IN23 IN31 IN32 IN33 IN34 BA11 BA12 BA21 DE11 DE12 DE13 DE14 DE15 GR11 GR12 GR13 GR21 GR22 GR31 GR32
1291 0 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1083 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3919 0 0 1 0 2 0 0 0 2 0 0 0 3 0 0 0 0 0 0 11 0 0 0
14685 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4021 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5452 0 0 1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
14686 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 2
4022 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1013 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2895 0 0 0 1 0 0 0 0 4 0 0 3 0 4 3 0 0 0 0 0 0 0 0
4719 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0
682 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0
3444 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1299 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0
2713 0 0 0 2 0 3 0 0 2 0 0 0 1 5 1 0 0 0 0 0 0 0 0
EP11 EP12 EP13 EP14 EP21 EP31 EP32 EP33 EP34 EP35 NE11 NE12 NE21 OT11 OT12 OT21 OT22 ecoval
1291 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1192
1083 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 424
3919 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 380
14685 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 370
4021 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 358
5452 0 0 0 0 0 0 1 0 0 11 0 0 0 0 1 0 0 356
14686 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 354
4022 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 346
1013 0 8 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 326
2895 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 325
4719 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 324
682 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 311
3444 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 306
1299 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 302
2713 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 302
[ reached getOption("max.print") -- omitted 166 rows ]
> data0<-sortdata100[sortdata100$ecoval<100,]
> data0<-na.omit(data0)
> data0
CV11 CV12 CV13 CV14 CV15 CV21 CV22 CV23 CV24 CV25 CV26 CV31 CV32 CV33 CV41 CV42 CV43 CV44 CV51 CV52 IN11 IN12 IN13
4728 0 0 0 1 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0
5339 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
11766 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
796 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3561 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
10581 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
10618 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 0 0 0 0 0
14376 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
14389 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
790 0 0 0 1 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 1 0 0
3974 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
4739 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0
156 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2740 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2950 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0
IN14 IN21 IN22 IN23 IN31 IN32 IN33 IN34 BA11 BA12 BA21 DE11 DE12 DE13 DE14 DE15 GR11 GR12 GR13 GR21 GR22 GR31 GR32
4728 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
5339 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
11766 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0
796 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3561 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10581 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
10618 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
14376 1 0 0 0 0 0 0 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 0
14389 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 0 0 0 0
790 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
3974 0 0 0 0 0 0 0 0 1 0 0 0 4 0 0 0 1 0 0 0 0 0 0
4739 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
156 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0
2740 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 0 0 0 0 0 0 0
2950 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
EP11 EP12 EP13 EP14 EP21 EP31 EP32 EP33 EP34 EP35 NE11 NE12 NE21 OT11 OT12 OT21 OT22 ecoval
4728 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 99
5339 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 99
11766 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 99
796 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98
3561 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98
10581 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 98
10618 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98
14376 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98
14389 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98
790 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 97
3974 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 97
4739 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 97
156 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96
2740 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 96
2950 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96
[ reached getOption("max.print") -- omitted 14984 rows ]
maybe something like this ?
library(dplyr)
data %>% group_by(ecoval > 100) %>% summarize_all(mean)
that should give you the average of each column for ecoval > and <= to 100
I am trying to make function that returns geometric mean with data.
I want to make loop with try() to pass valid data, but what i tried actually didn't worked.
This is function
R=function(g)
{
k=1
n=length(g)
for(i in 1 : n)
{
ifelse(g[i]>0, k<-k*g[i], stop("Negative component"))
k
}
t=k^(1/n)
t
}
And i want to use this function in this loop
set.seed(123)
data <- matrix(rnorm(10000, mean=3), ncol=25, dimnames=list(NULL, paste("X",
1:25, sep=".")))
v=rep(0,400)
for(i in 1 : 400)
{
try("v[i]=R(data[,i])",TRUE)
}
v
I want to get means for valid data, but it makes all value to 0
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[37] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[73] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[109] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[145] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[181] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[217] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[253] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[289] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[325] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[361] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[397] 0 0 0 0
Can you let me know where was wrong??
Thanks
I guess the problem is with the missing declaration of t as a numeric vector and the syntax of try() function. The following code should work, it worked for me.
R=function(g)
{
t = numeric(length(g))
k=1
n=length(g)
for(i in 1 : n)
{
ifelse(g[i]>0, k<-k*g[i], stop("Negative component"))
}
t=k^(1/n)
t
}
set.seed(123)
data <- matrix(rnorm(10000, mean=3), ncol=25, dimnames=list(NULL,paste("X",
1:25, sep=".")))
v=numeric(400)
for(i in 1 : 400)
{
try(v[i]<-R(data[i,]),TRUE)
}
v
I have the following sample data:
Hostname Date-Time hdisk86 hdisk88 hdisk90 hdisk89 hdisk91 hdisk92 hdisk93 hdisk94 hdisk96 hdisk95
1: hostname1 2015-01-26 00:15:22 0 0 0 0 0 0 0 0 0 0
2: hostname1 2015-01-26 00:30:24 0 0 0 0 0 0 0 0 0 0
3: hostname1 2015-01-26 00:45:25 0 0 0 0 0 0 0 0 0 0
4: hostname1 2015-01-26 01:00:25 0 0 0 0 0 0 0 0 0 0
5: hostname1 2015-01-26 01:15:28 0 0 0 0 0 0 0 0 0 0
6: hostname1 2015-01-26 01:30:29 0 0 0 0 0 0 0 0 0 0
hdisk98 hdisk97 hdisk99 hdisk100 hdisk101 hdisk102 hdisk103 hdisk108 hdisk107 hdisk104 hdisk105 hdisk109 hdisk110
1: 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk112 hdisk111 hdisk113 hdisk114 hdisk115 hdisk116 hdisk117 hdisk87 hdisk118 hdisk120 hdisk119 hdisk122
1: 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0
hdisk123 hdisk124 hdisk125 hdisk121 hdisk127 hdisk126 hdisk2 hdisk3 hdisk5 hdisk4 hdisk6 hdisk10 hdisk11 hdisk8
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk12 hdisk9 hdisk18 hdisk14 hdisk15 hdisk17 hdisk16 hdisk13 hdisk106 hdisk19 hdisk20 hdisk7 hdisk21 hdisk28
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk33 hdisk32 hdisk27 hdisk30 hdisk23 hdisk35 hdisk40 hdisk25 hdisk41 hdisk39 hdisk38 hdisk43 hdisk22 hdisk36
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk31 hdisk45 hdisk29 hdisk44 hdisk34 hdisk37 hdisk48 hdisk24 hdisk47 hdisk42 hdisk46 hdisk49 hdisk53 hdisk50
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk56 hdisk55 hdisk54 hdisk52 hdisk59 hdisk62 hdisk58 hdisk64 hdisk61 hdisk65 hdisk60 hdisk67 hdisk66 hdisk57
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk51 hdisk69 hdisk63 hdisk74 hdisk70 hdisk72 hdisk75 hdisk68 hdisk73 hdisk76 hdisk71 hdisk78 hdisk85 hdisk81
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk80 hdisk83 hdisk79 hdisk82 hdisk77 hdisk84 hdisk26 hdisk0 hdisk1 hdisk128 hdisk129 hdisk130 hdisk131 hdisk132
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk133 hdisk134 hdisk135 hdisk136 hdisk137 hdisk138 hdisk139 hdisk140 hdisk141 hdisk142 hdisk143 hdisk144
1: 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0
4: 0 0 0 0 0 0 0 0 0 0 0 0
5: 0 0 0 0 0 0 0 0 0 0 0 0
6: 0 0 0 0 0 0 0 0 0 0 0 0
hdisk145 hdisk146 hdisk147 hdisk148 hdisk149
1: 0 0 0 0 0
2: 0 0 0 0 0
3: 0 0 0 0 0
4: 0 0 0 0 0
5: 0 0 0 0 0
6: 0 0 0 0 0
What I'm trying to do is to take the mean, weighted.mean, and max values of each hdisk column, transpose this data to then sort by weighted.mean, max and mean. Then transpose back to plot in a bar chart. Here we go...
First taking the summary info (mean, weighted.mean, and max):
# Creating summary of I/O data (avg, wavg, max)...
c <- grep( "hdisk", names(DISKAVGRIO))
b <- c("Avg", "WAvg", "Max")
wavg = function(x) {
wavg.return <- weighted.mean(x, x)
if (is.nan(wavg.return)) {
return(0)
} else {
return(wavg.return)
}
}
my.summary = function(x) list(avg = mean(x), wavg = wavg(x), max = as.numeric(max(x)))
DT <- DISKAVGRIO[, lapply(.SD, my.summary), .SDcols=c]
DT[, `summary` := list("Avg", "WAvg", "Max")]
setcolorder(DT, c("summary", setdiff(names(DT), "summary")))
Them I have the following data table:
summary hdisk86 hdisk88 hdisk90 hdisk89 hdisk91 hdisk92 hdisk93 hdisk94 hdisk96 hdisk95 hdisk98 hdisk97 hdisk99
1: Avg 0 0 0 0 0 0 0 0 0 0 0 0 0
2: WAvg 0 0 0 0 0 0 0 0 0 0 0 0 0
3: Max 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk100 hdisk101 hdisk102 hdisk103 hdisk108 hdisk107 hdisk104 hdisk105 hdisk109 hdisk110 hdisk112 hdisk111
1: 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0
hdisk113 hdisk114 hdisk115 hdisk116 hdisk117 hdisk87 hdisk118 hdisk120 hdisk119 hdisk122 hdisk123 hdisk124
1: 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0
hdisk125 hdisk121 hdisk127 hdisk126 hdisk2 hdisk3 hdisk5 hdisk4 hdisk6 hdisk10 hdisk11 hdisk8 hdisk12 hdisk9
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk18 hdisk14 hdisk15 hdisk17 hdisk16 hdisk13 hdisk106 hdisk19 hdisk20 hdisk7 hdisk21 hdisk28 hdisk33 hdisk32
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk27 hdisk30 hdisk23 hdisk35 hdisk40 hdisk25 hdisk41 hdisk39 hdisk38 hdisk43 hdisk22 hdisk36 hdisk31 hdisk45
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk29 hdisk44 hdisk34 hdisk37 hdisk48 hdisk24 hdisk47 hdisk42 hdisk46 hdisk49 hdisk53 hdisk50 hdisk56 hdisk55
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk54 hdisk52 hdisk59 hdisk62 hdisk58 hdisk64 hdisk61 hdisk65 hdisk60 hdisk67 hdisk66 hdisk57 hdisk51 hdisk69
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk63 hdisk74 hdisk70 hdisk72 hdisk75 hdisk68 hdisk73 hdisk76 hdisk71 hdisk78 hdisk85 hdisk81 hdisk80 hdisk83
1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk79 hdisk82 hdisk77 hdisk84 hdisk26 hdisk0 hdisk1 hdisk128 hdisk129 hdisk130 hdisk131 hdisk132 hdisk133
1: 0 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0 0
hdisk134 hdisk135 hdisk136 hdisk137 hdisk138 hdisk139 hdisk140 hdisk141 hdisk142 hdisk143 hdisk144 hdisk145
1: 0 0 0 0 0 0 0 0 0 0 0 0
2: 0 0 0 0 0 0 0 0 0 0 0 0
3: 0 0 0 0 0 0 0 0 0 0 0 0
hdisk146 hdisk147 hdisk148 hdisk149
1: 0 0 0 0
2: 0 0 0 0
3: 0 0 0 0
Then I transform from wide to long:
# Converting from wide to long...
d <- grep("hdisk", names(DT), value = T)
DT_mdf <- melt(DT,
id.vars="summary",
measure.vars=d,
variable.name="hdisks",
value.name="percentage")
And get the following data table:
summary hdisks percentage
1: Avg hdisk86 0
2: WAvg hdisk86 0
3: Max hdisk86 0
4: Avg hdisk88 0
5: WAvg hdisk88 0
---
446: WAvg hdisk148 0
447: Max hdisk148 0
448: Avg hdisk149 0
449: WAvg hdisk149 0
450: Max hdisk149 0
Then, I try to transpose:
# Transpose to sort by wavg...
DT3 <- dcast(DT_mdf, summary ~ hdisks)
And I get the error message:
Using percentage as value column: use value.var to override.
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
'x' must be atomic
If I try to set value.var = percentage I get the following error message:
Error in match(x, table, nomatch = 0L) :
'match' requires vector arguments
Why this is not working? Aparently it suppose to work. Somebody has any idea?
Your function returns a list, and using lapply() on each column therefore results in each cell of the aggregated result as a list as well. You should be able to check this by looking at the class of all the columns. dcast() is looking for atomic type.
It's much more straightforward to get to your final result by using c() instead of list() in this case (note tested due to lack of MRE):
summary.funs = c("mean", "wavg", "max")
my.summary = function(x) c(mean(x), wavg(x), as.numeric(max(x)))
DT <- DISKAVGRIO[, lapply(.SD, my.summary), .SDcols=c][, summary := summary.funs]
should get you the result in the final format.
The Introduction to data.table vignette explains how to efficiently use j to get the data in the format you desire.
Also of use might be the Efficient reshaping using data.tables vignette.
For updates on vignettes, bookmark/check the Getting started page on project wiki. Also keep an eye on issue #944 and the CRAN data.table page for vignettes corresponding the current version.
I have two questions, the first is more complicated than the second.
I have a plot of my network below, but the plot is rather clustered how can I spread the nodes out more so I can clearly see the edges. I've tried a circular plot but I still got a rather clustered plot.
How can I rename the nodes? The current plot puts an 'X' in front of the node name, how can I remove the 'X'?
In my matrix an interacting node is marked with 1, non interacting nodes are marked with 0
Code:
library(igraph)
df <- as.matrix(read.table("sig_pairs_matrix_for_r.txt"))
g=graph.adjacency(df,mode="undirected",weighted=NULL,diag=FALSE)
plot.igraph(g,vertex.label=V(g)$name)
Matrix:
4 6 7 8 12 13 15 17 22 23 25 26 27 29 30 31 34 35 36 43 44 47 48 52 53 56 57 59 63 66 67 70 96 99 122 166 168 172 174 176 180 181 191 192 193 220 222 224 225 226 236 249 253 256 258 266 267 277 296
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 1 1 0 1 1 1 1 1 0 1 1 1 0 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 1 1 0 1 1 0 1 1 1 1 1 0 1 1 1 1 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
13 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
17 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
22 0 0 1 1 0 0 0 1 0 0 0 0 1 1 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
25 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
26 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
27 0 1 1 1 0 0 0 0 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
29 0 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
30 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
34 0 0 1 1 0 0 0 0 1 0 1 1 1 1 1 0 0 0 0 1 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
35 0 0 1 1 0 0 0 0 1 0 1 1 1 1 1 1 0 0 0 1 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
36 0 0 1 1 0 0 0 0 1 0 1 1 1 1 1 1 0 0 0 1 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
43 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
47 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
48 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
52 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
53 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
56 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
57 0 0 1 1 0 0 0 0 1 0 0 0 1 0 0 0 1 1 1 0 0 0 0 1 1 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
63 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
66 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
67 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
70 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
96 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
122 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
166 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
168 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
172 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
174 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
176 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
180 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
181 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 0 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
192 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
220 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0
222 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
224 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0
226 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0
236 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
249 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0
253 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 1 1 0 1 0
256 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
258 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 0 0 1 0 1 0
266 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 1 0
267 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
277 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 1 0 0 0
296 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
For the first question, check ?igraph::layout. There's some instructions how you can alter the aligment of nodes.
For your second question, I guess the graph takes the names of the nodes from the row or column names of your matrix but read.table by default appends names with prefix X in order to make names starting with number valid variable names (see make.names). So rownames of your matrix are actually X1, X2 etc. You can circumvent this by reading your matrix like this:
df <- as.matrix(read.table("sig_pairs_matrix_for_r.txt",check.names=FALSE))
Or you could rename the rows and columns of your matrix before making the graph, i.e.
#newnames is a vector containing the new names, such as c("a","b",...)
rownames(df)<-colnames(df)<-newnames
For the second part of your question I would create a separate files for the row and column names. Once imported you can set the column and row names.
temp = read.csv("adj_matrix.csv", sep=",",head=FALSE)
adjmatrix <- as.matrix(temp)
temprow = read.csv("rownames.csv", sep=",",head=FALSE)
rowns <-as.matrix(temprow)
tempcol = read.csv("colnames.csv", sep=",",head=FALSE)
cols <-as.matrix(tempcol)
rownames(adjmatrix)<- rows
colnames(adjmatrix)<- cols
g1 <- graph.adjacency(adjmatrix, mode=c("directed"), weighted=NULL, diag=TRUE)
plot.igraph(g1)