I'm trying to build an org chart from a data.frame in r using the data.tree package.
As far as i can tell i have constructed the tree correctly, but when I try to plot() the data.tree object (which print()s fine) I get an error:
abort(0) at jsStackTrace#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:5:22110
stackTrace#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:5:22258
abort#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:28:10656
nullFunc_iii#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:5:662065
a8#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:21:31634
iC#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:9:83383
aD#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:9:102098
uF#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:9:173805
pG#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:9:204484
xc#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:11:740
http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:28:403
ccallFunc#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:5:15982
http://localhost:30899/session/viewhtml2fdc215a4edd/lib/viz-0.3/viz.js:47:42
renderValue#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/grViz-binding-0.8.4/grViz.js:38:27
http://localhost:30899/session/viewhtml2fdc215a4edd/lib/htmlwidgets-0.7/htmlwidgets.js:625:30
forEach#[native code]
forEach#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/htmlwidgets-0.7/htmlwidgets.js:55:21
http://localhost:30899/session/viewhtml2fdc215a4edd/lib/htmlwidgets-0.7/htmlwidgets.js:551:14
forEach#[native code]
forEach#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/htmlwidgets-0.7/htmlwidgets.js:55:21
staticRender#http://localhost:30899/session/viewhtml2fdc215a4edd/lib/htmlwidgets-0.7/htmlwidgets.js:549:12
http://localhost:30899/session/viewhtml2fdc215a4edd/lib/htmlwidgets-0.7/htmlwidgets.js:638:38
Any ideas?
I have just started using the data.frame package a couple of days ago, but came across the same problem with some of my trees - print(tree) worked but plot(tree) gave a similar error message to yours. So far, I could always resolve the issue by removing special characters like single and double quotation marks from the input data. Thus, the plot function appears to be sensitive to certain symbols or special characters ... maybe a starting point for your search for a solution?
Related
I am very new to R and I would like to make UpSet plot of peptides.
I have five lists (sets) in .txt format (ID_list_vysledok_pos_vs_healthy_files.txt, ID_list_vysledok_pos_neg_files.txt, ID_list_vysledok_New_vs_Old_collumn_files.txt, ID_list_vysledok_neg_vs_healthy_files.txt, ID_list_vysledok_Coated_vs_Liquid_junction_files.txt)
Each .txt file is just list of peptides in this format: List of peptides
I was following step by step instructions by this link : http://genomespot.blogspot.com/2017/09/upset-plots-as-replacement-to-venn.html
The code is working without problems until I want to make the graph with : upset(res2, nsets=5)
It gives me following error: Error in upset_data(data, intersect, mode = mode, encode_sets = encode_sets, : unused argument (nsets = 5)
The res2 dataframe looks like it should be looking to make this graph : View(res2)
I think the problem is trivial and sets may not be properly defined (but in the link I was following it is working), but I was not able to fix this...
I installed these libraries : library(plyr), library(reshape2), library(UpSetR)
Just to be sure I will provide the code (same as in link): Photo of code
Thank you for any suggestions.
It looks like you might be mixing up packages. You are trying to use upset_data function from ComplexUpset package, but passing nsets argument which works with upset from UpSetR package. I would recommend taking a closer look at which functions you use. If you want to use both UpSetR and ComplexUpset, you can distinguish them with ComplexUpset::upset and UpSetR::upset.
The above error is occurring when trying to read a tree .
tree <- read.tree(paste0(table_dir,'tree.19.08.tre'))
I tried to reproduce the error but with other trees, for example with the iris example dataset it worked perfectly. The tree was generated with write.tree(tree, file='C:/Users/J/Desktop/proj/d/t/tree.19.08.tre',append = FALSE). I can look at tree in the programme FigTree (javascript based). Maybe it looks a bit strange but why can´t I open it in R?
Any suggestions?
That is a cutout of tree in figtree, in case it helps ;)
That is the full error:
Fehler in FUN(X[[i]], ...) : numbers of left and right parentheses in Newick string not equal
3.
FUN(X[[i]], ...)
2.
lapply(STRING, .treeBuild)
1.
read.tree(paste0(table_dir, "tree.19.08.tre"))
I had the same problem and I couldn't load it with DECIPHER either, but I made it with phytools:
library(phytools)
tree = read.newick(treeFileName)
Exploring the loaded phylo object I realized that the tree was not correct, the reason being that the leaves of the tree contained in the name semicolons, as it is costumary in some taxonomic formats, e.g.
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria
and the problem is that the semicolon indicates the end of the tree in newick format. Simply transforming the semicolons into other symbol, e.g.
d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria
solved the problem.
I've got exactly the same error when loading a tree I got from a colleague.
But I was able to load it using
tree <- DECIPHER::ReadDendrogram(treeFileName)
I'm unable to save a plot generated by the plot.Node function in data.tree. I've tried the following:
### Create tree object and plot it
data(acme);
plot(acme);
This works fine, showing the plot, as one would expect.
### Try saving it as png
png(filename='file.png', type='cairo-png');
plot(acme);
dev.off();
This creates an empty file. ggsave does the same. Apparantly, plot.Node uses DiagrammeR under the hood, so I looked into that package. It has a function to export graphs:
export_graph(acme, file_name="file.png");
This gives the error:
Error in file.exists(diagram) : invalid 'file' argument
When I transform to GraphViz first, I get a different error:
export_graph(ToGraphViz(acme), file_name="file.png");
Error in graph$dot_code : $ operator is invalid for atomic vectors
Clearly, exporting to GraphViz doesn't quite export to what DiagrammeR expects.
I'm in RStudio and so could in theory just save the plot using the GUI, but I need this for in a script.
Apparently, plot.Node doesn't actually plot anything - instead it seems to generate html/js. Does this mean that that result cannot be stored as a graphic? Or is there some export/conversion function somewhere that I'm completely missing? it certainly feels like I'm missing something obvious - I assume the need to store plotted data.trees as images is quite common. But I have no idea which potential solutions I can still explore.
I'd be very grateful for any pointers anybody has!
As sebastian-c suggested, things work now a bit differently than suggested by Matherion, as of R 3.3.3 with data.tree 0.7.0 and DiagrammeR 0.9.0
Pre-requisite: DiagrmmeRsvg and dependencies need to be installed. Depending on your OS, for this to work you might have to install V8. For example on ubuntu:
apt-get install libv8-3.14-delibv8-3.14-dev
And then in R:
install.packages("DiagrammeRsvg")
On Windows, I didn't have to install anything (maybe because Chrome is installed?).
Once DiagrammeRsvg is available, run:
library(data.tree)
data(acme)
library(DiagrammeR)
export_graph(ToDiagrammeRGraph(acme), "export.pdf")
I've found the answer, at least, partially. There exists a package dedicated to exporting GraphViz diagrams to SVG: DiagrammeRsvg.
So this works:
treeAsSVG <- export_svg(grViz(ToGraphViz(acme)));
writeLines(treeAsSVG, "filename.svg"));
The grViz is necessary to actually convert the ToGRaphViz output to something that can be interpreted by export_svg. I'm still not really sure (yet) what all goes on under the hood - for example, this does not work:
export_graph(grViz(ToGraphViz(acme)), file_name="filename.svg");
But, if anybody else has a similar problem and stumbles upon this question, perhaps this partial answer can help them to at least export something that can then be integrated in e.g. html pages.
By converting acme with as.phylo() it works, but it looks a little boring:
plot(as.phylo(acme),
show.node.label=TRUE,
node.pos=2,
no.margin=TRUE
)
# adding edge labels
edgelabels(as.vector(acme$Get("cost"))[-1],
adj = c(0,-0.5),
frame = "none")
solution with as.phylo()
I also tried as.igraph. However, the nodes overlap and it looks even less pretty:
plot(0, type="n", ann=FALSE, axes=FALSE,
xlim=extendrange(ig[,1]),
ylim=extendrange(ig[,2]))
plot(ig,
layout=layout_as_tree(ig,root=1),
vertex.shape="rectangle",
vertex.size=(strwidth(V(ig)$name) + strwidth("oo")) * 100,
#vertex.size2=strheight("I") * 2 * 100,
edge.label=acme$Get("p",traversal = "level")[-1]
)
solution with as.igraph()
I am trying to use the package paleotree to build LTT plots, but I get the following error when I try to input my trees.
a=read.tree(file.choose()) # to choose newick/nexus file
multiDiv(a)
Error in multiDiv(a) : Data of Unknown Type
Does paleotools only take objects of class 'multiphylo' ? I converted the imput tree to class multiphylo, but it still gives the same error. Can anyone suggest how to go about it?
I'm the author of package paleotree. I think what is going on here is that you are passing a single tree to multiDiv, which is setup for analyzing lists of objects, each of which are converted to a diversity curve. You probably want phyloDiv() instead. I can't be certain without know more about your data.
I am having a hard time coding in R language. What I am trying to do is read large amount of data in to one data frame, and make pretty pictures.
This is what I have:
# assign data
file_name1<-"data1_txt"
file_name2<-"data2_txt"
data.dir<-"/...../Documents/R programing Language/"
for(i in 1:length(1)){
newData1<-read.table(file.path(data.dir, file_name1))
#Replace negative numbers with NA
xx <- which(datavalues<0)
datavalues[xx] <- NA
newData2<-read.table(file.path(data.dir,file_name2))
}
Error I have is:
Error in read.table(file.path(data.dir, file_name1)) :
no lines available in input
I am trying to figure out by myself, but I am very new to R language, and I don't have enough knowledge of functions in R. Please explain what this error means and advice on my coding.
Thank you very much,
Uka
Similar situation was solved here with similar question (I know this post is quite old). Recently I got such error parsing several files... The reason was some files were empty which makes sense of error message.
Anyway, just make sure your input will not be empty using try ou trycatch as suggested on mentioned link.