Question: R plot error
gravatar for megha.24may
3.4 years ago by
megha.24may0 wrote:

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

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by megha.24may0

What code are you using?  Any errors?  What is the output of sessionInfo()?

ADD REPLYlink written 3.4 years ago by Sean Davis21k

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

 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8    
 [7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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 
ADD REPLYlink written 3.4 years ago by megha.24may0

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

ADD REPLYlink written 3.4 years ago by megha.24may0

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(bitmapType = "cairo")


ADD REPLYlink written 3.4 years ago by James W. MacDonald48k

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

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by megha.24may0
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