R plot error
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@megha24may-7791
Last seen 5.9 years ago
india

hello everyone , 

whenever i am trying to plot in R. Any R plot labels don't show up instead of text it just shows some blank boxes.

so can you suggest me something ?

 

thnkx Megha Varshney

r bioconductor graph plot data representation in graphical forms • 1.1k views
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What code are you using?  Any errors?  What is the output of sessionInfo()?

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the session info is here and i am trying to plot correlation values.. but the same problem is also occurring with simple box plot and histograms.

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8    
 [5] LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8   
 [7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] lattice_0.20-31       cummeRbund_2.8.2      Gviz_1.10.11         
 [4] rtracklayer_1.29.6    GenomicRanges_1.21.12 GenomeInfoDb_1.5.6   
 [7] IRanges_2.3.8         S4Vectors_0.7.3       fastcluster_1.1.16   
[10] reshape2_1.4.1        ggplot2_1.0.1         RSQLite_1.0.0        
[13] DBI_0.3.1             BiocGenerics_0.15.1  

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_0.1.5 VariantAnnotation_1.15.10
 [3] splines_3.2.0              colorspace_1.2-6          
 [5] GenomicFeatures_1.21.7     XML_3.98-1.1              
 [7] survival_2.38-1            foreign_0.8-63            
 [9] BiocParallel_1.3.13        RColorBrewer_1.1-2        
[11] lambda.r_1.1.7             matrixStats_0.14.0        
[13] plyr_1.8.2                 stringr_1.0.0             
[15] zlibbioc_1.15.0            Biostrings_2.37.2         
[17] munsell_0.4.2              gtable_0.1.2              
[19] futile.logger_1.4.1        latticeExtra_0.6-26       
[21] Biobase_2.29.1             biomaRt_2.25.1            
[23] AnnotationDbi_1.31.9       proto_0.3-10              
[25] Rcpp_0.11.6                acepack_1.3-3.3           
[27] scales_0.2.4               BSgenome_1.37.1           
[29] Hmisc_3.16-0               XVector_0.9.1             
[31] Rsamtools_1.21.5           gridExtra_0.9.1           
[33] digest_0.6.8               stringi_0.4-1             
[35] biovizBase_1.14.1          tools_3.2.0               
[37] bitops_1.0-6               magrittr_1.5              
[39] RCurl_1.95-4.6             dichromat_2.0-0           
[41] Formula_1.2-1              cluster_2.0.1             
[43] futile.options_1.0.0       MASS_7.3-40               
[45] rpart_4.1-9                GenomicAlignments_1.5.9   
[47] nnet_7.3-9 
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actually in starting i was getting some error and on internet i get solution that is

sudo yum install xorg-x11-fonts-75dpi.noarch and sudo yum install xorg-x11-fonts-100dpi.noarch then suddenly i notice this problem

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My understanding is that R is supposed to use the cairo device by default, but I have also had problems plotting (using Ubuntu), where it seems to want to use X11 instead. I have had good results forcing R to use cairo, by putting this in my .Rprofile file:

setHook(packageEvent("grDevices", "onLoad"),
    function(...) grDevices::X11.options(type='cairo'))
options(device='x11')
options(bitmapType = "cairo")

 

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no still I am not getting any label in plot instead of that it just showing some blank boxes.

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