Hi I am using DiffBind's dba.plotHeatmap() or just plot() to plot a correlation matrix between the peak calls.
For my correlation matrix I don't want to have the axis labels and thus used the given command
plot(DBdata,labRow = NULL, labCol = NULL)
but getting the following error:
Error in heatmap.3(domap, labCol = collab, col = cols, trace = "none", :
formal argument "labRow" matched by multiple actual arguments
For details you can visit this page for DiffBind [source core.R][1] which also incorporated heatmap.3().
Can anyone help me in this regard? Thanks in advance.
Also have a look of my sessionInfo().
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_rt.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ggplot2_3.2.1 DiffBind_2.13.0
[3] SummarizedExperiment_1.15.3 DelayedArray_0.11.2
[5] BiocParallel_1.19.0 matrixStats_0.54.0
[7] Biobase_2.45.0 GenomicRanges_1.37.12
[9] GenomeInfoDb_1.21.1 IRanges_2.19.10
[11] S4Vectors_0.23.13 BiocGenerics_0.31.4
loaded via a namespace (and not attached):
[1] Category_2.51.0 bitops_1.0-6 bit64_0.9-7
[4] RColorBrewer_1.1-2 progress_1.2.2 httr_1.4.0
[7] Rgraphviz_2.29.0 tools_3.6.0 backports_1.1.4
[10] R6_2.4.0 KernSmooth_2.23-15 DBI_1.0.0
[13] lazyeval_0.2.2 colorspace_1.4-1 withr_2.1.2
[16] tidyselect_0.2.5 prettyunits_1.0.2 bit_1.1-14
[19] curl_3.3 compiler_3.6.0 graph_1.63.0
[22] rtracklayer_1.45.1 checkmate_1.9.3 caTools_1.17.1.2
[25] scales_1.0.0 genefilter_1.67.1 RBGL_1.61.0
[28] askpass_1.1 rappdirs_0.3.1 stringr_1.4.0
[31] digest_0.6.20 Rsamtools_2.1.2 AnnotationForge_1.27.0
[34] XVector_0.25.0 pkgconfig_2.0.2 BSgenome_1.53.0
[37] dbplyr_1.4.2 limma_3.41.5 rlang_0.4.0
[40] RSQLite_2.1.1 GOstats_2.51.0 hwriter_1.3.2
[43] gtools_3.8.1 dplyr_0.8.3 VariantAnnotation_1.31.3
[46] RCurl_1.95-4.12 magrittr_1.5 GO.db_3.8.2
[49] GenomeInfoDbData_1.2.1 Matrix_1.2-17 Rcpp_1.0.2
[52] munsell_0.5.0 yaml_2.2.0 stringi_1.4.3
[55] edgeR_3.27.5 debugme_1.1.0 zlibbioc_1.31.0
[58] gplots_3.0.1.1 BiocFileCache_1.9.1 grid_3.6.0
[61] blob_1.2.0 ggrepel_0.8.1 gdata_2.18.0
[64] crayon_1.3.4 lattice_0.20-38 splines_3.6.0
[67] Biostrings_2.53.0 GenomicFeatures_1.37.1 annotate_1.63.0
[70] hms_0.5.0 batchtools_0.9.11 locfit_1.5-9.1
[73] zeallot_0.1.0 pillar_1.4.2 rjson_0.2.20
[76] systemPipeR_1.19.1 base64url_1.4 biomaRt_2.41.7
[79] XML_3.98-1.20 glue_1.3.1 ShortRead_1.43.0
[82] latticeExtra_0.6-28 data.table_1.12.2 vctrs_0.2.0
[85] gtable_0.3.0 openssl_1.4 purrr_0.3.2
[88] amap_0.8-17 assertthat_0.2.1 xtable_1.8-4
[91] survival_2.44-1.1 pheatmap_1.0.12 tibble_2.1.3
[94] GenomicAlignments_1.21.2 AnnotationDbi_1.47.0 memoise_1.1.0
[97] brew_1.0-6 GSEABase_1.47.0
DiffBind
package has neither theplot()
function (or any methods thatplot()
dispatches to) nor does it have theheatmap.3
function.Can you please edit your question and add the output of
sessionInfo()
(and also clean up the formatting a bit)?. What would also help are the outputs tofind("heatmap.3")
andfind("plot")
.Dear Ramrs, I have made the suggested changes to my post.
DiffBind do have dba.plotHeatmap() or just plot() to plot correlation matrix which uses heatmap.3 in background as mentioned in the source code core.R
I hope this will be helpful in seeking your help.
@Rory Stark , can you please help?
Thanks