Error: ggplot2 doesn't know how to deal with data of class matrix

[sean-la]

I'm currently testing my installation of DangerTrack. I ran sh prepare.sh successfully, but when I run Rscript summarize.R, I get the following messages in stderr:

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

[1] "summary.1KG.5000.txt"                   
[2] "summary.ENCODE_DAC_blacklisted.5000.txt"
[3] "summary.GIAB.5000.txt"                  
[4] "summary.GRC_issues.5000.txt"            
[5] "summary.map100mer.5000.txt"             
[6] "summary.map50mer.5000.txt"              
[1] 619150      7
                       #BIN events_1KG ENCODE_DAC_blacklisted events_GIAB
1              chr10:0-5000          0                      0           0
2         chr10:10000-15000          0                      0           0
3       chr10:100000-105000          1                      0           0
4     chr10:1000000-1005000          1                      0           0
5   chr10:10000000-10005000          0                      0           0
6 chr10:100000000-100005000          0                      0           0
  GRC_issues Mapability100mer Mapability50mer
1          1         0.000000       0.0000000
2          1         0.000000       0.0000000
3          1         0.570697       0.3202720
4          1         0.923622       0.8365010
5          0         0.195906       0.0307765
6          0         1.000000       0.9676170
Warning message:
Removed 1 rows containing non-finite values (stat_bin). 
[1] 10000     4
       events_1KG events_GIAB Mapability100mer Mapability50mer
440289          2           0         0.978955        0.933754
251460          1           0         1.000000        0.974464
535266          0           0         0.999700        0.846184
262436          0           2         0.996842        0.837239
220858          0           0         0.998138        0.888584
276971          1           0         0.999367        0.906750
Error: ggplot2 doesn't know how to deal with data of class matrix
Execution halted

Thanks!

[sean-la]

For what it's worth, I also get the following output in stdout:

[1] "summary.1KG.5000.txt"                   
[2] "summary.ENCODE_DAC_blacklisted.5000.txt"
[3] "summary.GIAB.5000.txt"                  
[4] "summary.GRC_issues.5000.txt"            
[5] "summary.map100mer.5000.txt"             
[6] "summary.map50mer.5000.txt"              
[1] 619150      7
                       #BIN events_1KG ENCODE_DAC_blacklisted events_GIAB
1              chr10:0-5000          0                      0           0
2         chr10:10000-15000          0                      0           0
3       chr10:100000-105000          1                      0           0
4     chr10:1000000-1005000          1                      0           0
5   chr10:10000000-10005000          0                      0           0
6 chr10:100000000-100005000          0                      0           0
  GRC_issues Mapability100mer Mapability50mer
1          1         0.000000       0.0000000
2          1         0.000000       0.0000000
3          1         0.570697       0.3202720
4          1         0.923622       0.8365010
5          0         0.195906       0.0307765
6          0         1.000000       0.9676170
[1] 10000     4
       events_1KG events_GIAB Mapability100mer Mapability50mer
320193          0           0         0.991796        0.947221
119418          0           0         1.000000        0.968683
329841          0           0         1.000000        0.957862
201044          0           0         0.961997        0.568092
272139          0           0         1.000000        0.980700
191279          0           0         1.000000        0.905309

[fritzsedlazeck]

what R version are you using?

[igordot]

And also what version of ggplot2?

[sean-la]

R version: 3.3.1 ggplot2: 2.2.1

[igordot]

Looks like that was from the correlations plot that we ended up not using in the end, so that error is real and evaded detection.

Anyway, it should be fixed now. Try the latest version.

[sean-la]

It works now, thanks!