Correlation plot error

Question

[1769mkc]

I m trying to make a correlation plot but Im getting error Error in eval(expr, envir, enclos) : object 'Var1' not found

My data frame is called S5

Below is my R code which I'm using to make the plot

corr <- round(cor(S5), 1)
ggcorrplot(corr)

` Please let me know what is going wrong if try to head the corr object I see nothing called Var1 object .So let me know what is going wrong ,since I can see the corr computed matrix .

My data frame is as such I mean its just a subset of my data set

Gene     `7256_Mono` `7653_Mono` `6792_Mono` `6792_HSC` 

SMARCA4   24.30380    53.72460    30.44740   23.52570   
SMARCA2   16.30570    20.33060    23.92220   55.04900

[Devon Ryan]

Have you tried cor.matrix() rather than cor()?

[1769mkc]

no i haven't ,i will try your suggestion

[ddiez]

Uh? Don't know cor.matrix().

[Devon Ryan]

Neither do I, but it's made reference to in the help for ggcorrplot, so my presumption is that it produces some sort of S4 object that's needed for the plotting.

[ddiez]

I see! I imagined there was a method in ggcorrplot before asking but couldn't find it. There is however a cor_pmat() function. Maybe you checked an older documentation? I have ggcorrplot version 0.1.1 installed. Probably it was cor.matrix() first and they changed it because it may confuse the S3 dispatch method (again, just guessing).

[ddiez]

Cannot replicate this (please, try to include an example that we can run and obtain the same error as you do. aka. a minimum reproducible example). However, in my try I assigned the column "Gene" as row names. If you data is a data.frame like the one you included you cannot use cor() since that will give a Error in cor(d) : 'x' must be numeric error.

[1769mkc]

well too much technical details I would be really glad if you guys can give me help , with my error , even if I removing the first column that corresponds to my gene name I still get the error when i'm trying to plot.

"cor() since that will give a Error in cor(d) : 'x' must be numeric error."

[ddiez]

This works for me:

d <- read.table(header = TRUE, row.names = 1, text = 
"Gene     `7256_Mono` `7653_Mono` `6792_Mono` `6792_HSC` 
SMARCA4   24.30380    53.72460    30.44740   23.52570   
SMARCA2   16.30570    20.33060    23.92220   55.04900")

ggcorrplot::ggcorrplot(cor(d))

[1769mkc]

Im still getting the same error Error in eval(expr, envir, enclos) : object 'Var1' not found I just copy and paste your code but I do get that error I posted

[Devon Ryan]

You'll need to post a complete reproducible example, including the output of sessionInfo().

[1769mkc]

R version 3.2.3 (2015-12-10)

Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS

locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_IN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] ggcorrplot_0.1.1 gplots_3.0.1 pheatmap_1.0.8 readr_1.0.0 tidyr_0.6.1 reshape2_1.4.2
[7] ggplot2_2.2.1 reshape_0.8.6 Biobase_2.30.0 BiocGenerics_0.16.1 RISmed_2.1.6

loaded via a namespace (and not attached): [1] splines_3.2.3 gtools_3.5.0 Formula_1.2-1 assertthat_0.1
[5] stats4_3.2.3 latticeExtra_0.6-28 BSgenome_1.38.0 coin_1.1-3
[9] Rsamtools_1.22.0 corrplot_0.77 RSQLite_1.1-2 backports_1.0.5
[13] lattice_0.20-34 biovizBase_1.18.0 digest_0.6.12 GenomicRanges_1.22.4
[17] RColorBrewer_1.1-2 XVector_0.10.0 checkmate_1.8.2 colorspace_1.3-2
[21] sandwich_2.3-4 htmltools_0.3.5 Matrix_1.2-8 R.oo_1.21.0
[25] plyr_1.8.4 XML_3.98-1.5 biomaRt_2.26.1 zlibbioc_1.16.0
[29] mvtnorm_1.0-5 scales_0.4.1 gdata_2.17.0 BiocParallel_1.4.3
[33] htmlTable_1.9 tibble_1.2 cummeRbund_2.12.1 IRanges_2.4.8
[37] party_1.1-2 TH.data_1.0-8 SummarizedExperiment_1.0.2 GenomicFeatures_1.22.13
[41] nnet_7.3-12 Gviz_1.14.7 lazyeval_0.2.0 strucchange_1.5-1
[45] survival_2.40-1 magrittr_1.5 memoise_1.0.0 R.methodsS3_1.7.1
[49] MASS_7.3-45 foreign_0.8-67 tools_3.2.3 data.table_1.10.0
[53] matrixStats_0.51.0 multcomp_1.4-6 stringr_1.1.0 S4Vectors_0.8.11
[57] munsell_0.4.3 cluster_2.0.5 AnnotationDbi_1.32.3 lambda.r_1.1.9
[61] Biostrings_2.38.4 GenomeInfoDb_1.6.3 caTools_1.17.1 futile.logger_1.4.3
[65] grid_3.2.3 RCurl_1.95-4.8 dichromat_2.0-0 VariantAnnotation_1.16.4
[69] htmlwidgets_0.8 labeling_0.3 bitops_1.0-6 base64enc_0.1-3
[73] codetools_0.2-15 gtable_0.2.0 DBI_0.5-1 R6_2.2.0
[77] GenomicAlignments_1.6.3 gridExtra_2.2.1 zoo_1.7-14 dplyr_0.5.0
[81] knitr_1.15.1 rtracklayer_1.30.4 Hmisc_4.0-2 futile.options_1.0.0
[85] KernSmooth_2.23-15 modeltools_0.2-21 stringi_1.1.2 Rcpp_0.12.9
[89] rpart_4.1-10 acepack_1.4.1

[ddiez]

OK, your relevant packages seem up-to-date. Only difference with my system is that your R version is more than one year old, but probably that is not the problem. Did you try R --vanilla? Do you still get the same error then?

[ddiez]

OK, then I am going to suggest a few options.

1. Make sure you have your packages up-to-date. ggplot2 was heavily update some months ago and the problem might be related to that.
2. Make sure there are not name masking errors. Try running R in vanilla (i.e. in the terminal type R --vanilla). Load just ggcorrplot and try the code above.
3. After you get the error type traceback() and report the output here.
4. Type sessionInfo() and report the output.

[1769mkc]

0: eval(expr, envir, enclos)
9: FUN(X[[i]], ...)
8: lapply(aesthetics, eval, envir = data, enclos = plot$plot_env)
7: f(..., self = self)
6: l$compute_aesthetics(d, plot)
5: f(l = layers[[i]], d = data[[i]])
4: by_layer(function(l, d) l$compute_aesthetics(d, plot))
3: ggplot_build(x)
2: print.ggplot(x)
1: function (x, ...) 


UseMethod("print")(x)

Answer 1

[agnkwi06]

In my case loading library 'reshape' before running the code was creating this problem.