WGCNA_ problem in creating scale free topology plot
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@amit-kumar-subudhi-6098
Last seen 7.1 years ago
Dear Dr. Langfelder, Trying to generate a coexpression based systems network using WGCNA R package. An adjacency matrix was generated from an expression matrix using the command softPower = 8; adjacency = adjacency(datExpr, power = softPower); Then I tried to see whether the network is exhibiting scale free topology or not using the command scaleFreePlot(adjacency, nBreaks = 10, truncated = FALSE, removeFirst = FALSE, main = paste("scale free topology"), xlab = "log10(k)", ylab = "log10(p(k))") but in return I am getting the following error message Error in plot.defaultlog.dk, log.p.dk, xlab = "log10(k)", ylab = "log10(p(k))", : formal argument "xlab" matched by multiple actual arguments Please let me know where I am going wrong. I have successfully used most of the codes to visualize network and generate modules. With best regards Amit -- Amit Kumar Subudhi Research Scholar, CSIR-Senior Research Fellow, Molecular Parasitology and Systems Biology Lab, Department of Biological Sciences , FD III, BITS, Pilani, Rajasthan- 333031 e mail- amit4help@gmail.com amit.subudhi@pilani.bits-pilani.ac.in Mob No- 919983525845 [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 16 hours ago
United States
Hi Amit, On 6/20/2014 3:46 AM, amit kumar subudhi wrote: > Dear Dr. Langfelder, > > Trying to generate a coexpression based systems network using WGCNA R > package. > > An adjacency matrix was generated from an expression matrix using the > command > softPower = 8; > adjacency = adjacency(datExpr, power = softPower); > > Then I tried to see whether the network is exhibiting scale free topology > or not using the command > > scaleFreePlot(adjacency, nBreaks = 10, truncated = FALSE, removeFirst = > FALSE, main = paste("scale free topology"), xlab = "log10(k)", ylab = > "log10(p(k))") > > but in return I am getting the following error message > > Error in plot.defaultlog.dk, log.p.dk, xlab = "log10(k)", ylab = > "log10(p(k))", : > formal argument "xlab" matched by multiple actual arguments > > Please let me know where I am going wrong. Note that there is no xlab, nor ylab arguments for scaleFreePlot(), but there is an ellipsis argument (...), which allows you to pass arbitrary arguments to other functions within scaleFreePlot(). If you look at the scaleFreePlot() function body, you will see this near the bottom: suppressWarningsplotlog.dk, log.p.dk, xlab = "log10(k)", ylab = "log10(p(k))", main = title, ...)) where there is a call to plot() that has existing xlab and ylab arguments (that are identical to the ones you are attempting to pass in), as well as another ellipsis argument, which allows your xlab and ylab arguments to be passed to plot() as well. So the plot function is seeing two arguments for xlab and ylab, and then errors out because it only expects one. The easy (and only) fix for this is to remove the xlab and ylab arguments from your call to scaleFreePlot(). Best, Jim > > I have successfully used most of the codes to visualize network and > generate modules. > > With best regards > Amit > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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