[R] Igraph library: How to calculate APSP (shortest path matrix) matrix for a subset list of nodes.
Dear R Users, I have a network of 25000 total nodes and a list of 500 node which is a subset of all nodes. Now I want to calculate the APSP (all pair shortest path) matrix only for these 500 nodes. I would appreciate any help. Thanks in advance Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Subset of matrix
Dear R users I have a big matrix like 6021118879029011741015199066136288 100714 602110.6580.6880.4740.2620.1630.1370.32 0.2520.206 11880.65810.9170.2450.3310.1220.1480.194 0.1680.171 7900.6880.91710.2430.310.1220.150.19 0.1710.174 2900.4740.2450.24310.390.3190.1870.4 0.3110.235 11740.2620.3310.310.3910.2950.3520.345 0.3060.308 10150.1630.1220.1220.3190.29510.4210.343 0.4420.435 19900.1370.1480.150.1870.3520.42110.313 0.380.395 66130.320.1940.190.40.3450.3430.31310.58 0.429 62880.2520.1680.1710.3110.3060.4420.380.58 10.723 1007140.2060.1710.1740.2350.3080.4350.395 0.4290.7231 59510.220.1680.1710.2670.3180.4780.4090.478 0.8440.85 59600.2320.1830.1860.2720.3240.420.3830.522 0.6860.711 2360.2590.2130.2180.2830.3570.3820.40.549 0.6550.608 649560.1990.1720.1750.250.3550.4440.4750.523 0.6330.614 2390.1880.1690.1730.2370.3620.4630.50.469 0.5960.692 330320.250.1670.1690.3080.3010.4070.3460.486 0.6550.64 62620.2540.1780.1820.3140.3290.3960.360.459 0.6790.633 59610.2620.1890.1940.3110.3420.3620.3770.468 0.6210.574 59620.2430.1770.180.2980.3240.3890.3530.453 0.6670.62 63060.2260.1680.1710.2740.3060.3890.380.514 0.6980.62 61060.2260.1680.1710.2740.3060.3890.380.514 0.6980.62 62870.2080.1750.1780.250.3280.4290.4220.529 0.7710.689 59500.1930.1750.1790.230.3440.4650.50.448 0.7330.816 8330.3120.2440.2420.4080.4440.3280.3170.526 0.5620.517 7500.1680.1550.1570.2080.3390.5140.5150.385 0.5780.722 61370.2010.1680.1710.2390.3060.3890.380.453 0.6980.62 1457420.3170.2290.2360.3490.3250.3390.305 0.5190.5810.534 58100.3640.2160.2210.4110.2940.3380.2690.603 0.6310.47 8250.3640.2160.2210.4110.2940.3380.2690.603 0.6310.47 74050.3130.2460.2440.3550.3670.290.3170.537 0.5070.484 10450.1330.1240.1350.1980.3330.4410.3440.277 0.3620.341 11230.110.1060.1040.1570.2620.4150.3680.227 0.3040.333 5880.2810.3120.340.3030.4190.2780.40.287 0.3120.316 with more than thousand number of rows and column I want to extract or subset a child matrix from above with specific row names or col names. e.g. For above matrix I need only rows which has following row names. 5951 236 6306 5950 145742 1123 I would appreciate if you can use this matrix as input. Thanks in advance. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Alignment and Reshaping of the matrix
Dear R users, I have a matrix like 85 .90 86 .89 87 .98 86 .87 88 .98 90 .78 88 .76 89 .56 90 .67 95 .67 89 .89 90 .87 91 .56 96 .87 90 .76 92.98 each pair of columns present a variable name and next the value. I have matrix with more than 500 rows and column. Now I want to convert this matrix in to. 85 .90 00 .00 00 86 .00 .89 .00 .87 87 .00 00 .98 00 88 .98 00 .76 00 89 .00 00 .89 .56 90 .67 .78 .76 .87 91 .56 00 .00 00 92 .00 .00 .00 .98 93 .00 .0000 00 94 .00 .0000 00 95 .00 .6700 00 96 .00 .8700 00 Where first column represent the Variable name. And if the first matrix is transposed, then how to get the output in which First raw present the variable name. It will be great help for my research. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Two Colored Heatmap
Hi All I have matrix Like:- 10 20 40 60 100 Glucose UP Down UP No UP Fructose UP UP Down UP No Sucrose UP Down UP No Down Taurine No No No No UP Cellobiose Up NoUp Down No TrehaloseNo UpUp Down Up First raw and first column are labels. Each column present a condition. I want to create a heatmap which colored UP = RED, Down= Blue and No= White. Thanks in Advance. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] For Subset or Reshaping the Table
Hi R users I am a new user in the field of R. I want to subset or reshape a data.frame. For example I have a matrix like A B C D E F G a 1 2 3 4 5 6 7 b 4 6 8 9 5 5 6 c 3 4 4 4 3 3 6 d 1 2 4 6 8 8 9 e 5 6 7 8 9 2 3 I want to reshape the matrix in this format Row Col Value a D 4 a E 5 a F 6 .. .. e E 9 I want only the pair which pass a threshold for example >3. Please help me. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reshape a matrix
Dear R users, I have a matrix like A X1 B Y2 C Z3 I want to reshape this matrix into this format X Y Z A 1 B 2 C 3 Thanks in advance for your help. Dinesh -- Dinesh Kumar Barupal Junior Specialist Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] similarity matrix to dendrogram (GML format)
Dear R users I have a similarity matrix of 100X100 (chemical similarity). Now I want to create a dendrogram from it and export this dendrogram as GML format network. Can you please reply How I can do this stuff? Thanks in advance. Dinesh -- Dinesh Kumar Barupal Junior Specialist Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
