Hi there,
I am trying to make volcano plot using EnhancedVolcano to mark the gene label (using selectLab function) in different colours, but fail to do so. I have also looked into the suggestion in https://github.com/kevinblighe/EnhancedVolcano#highlighting-key-variables-via-custom-point-sizes, but with no luck.
I found out some functionality (e.g labCol, subtitle, caption, shape, pointSize, boxedlabels, drawConnectors, widthConnectors) in my session did not work, and return the below:
Error in EnhancedVolcano(res.annotA, lab = gene_nameAV, x = "log2FoldChange", :
unused argument (labCol = "blue"), etc
Not sure if it is a version (1.0.1) problem...
How could I upgrade the version? as the BiocManager::install('EnhancedVolcano') only install this older version for my R Packrat.
========================================================
Though I can still plot the basic function with the following functionalities:
EnhancedVolcano(res.annotA,
lab = gene_nameA,
x = 'log2FoldChange',
y = 'padj',
selectLab = gene_nameA_selected,
xlim = c(-3, 11),
ylim = c(-1, 35),
xlab = bquote(~Log[2]~ 'fold change'),
ylab = bquote(~-Log[10]~adjusted~italic(P)),
title = 'XXX',
pCutoff = 0.05,
FCcutoff = 1.0,
transcriptPointSize = 1.5,
transcriptLabSize = 4.0,
col=c('black', 'orange', 'red3', 'green'),
colAlpha = 1,
cutoffLineType = 'dotted',
cutoffLineCol = 'grey50',
cutoffLineWidth = 0.8,
legend=c("Not significant","Log|Fold Change|>1","adj-p<0.05","adj-p<0.05 & Log|Fold Change|>1"),
legendPosition = 'bottom',
legendLabSize = 13,
legendIconSize = 2.0,
colConnectors = 'grey30'
)
Any idea on how to highlight certain gene label/point (in different shape/colour) would be very much appreciated :)
====================
Here is my sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] grDevices datasets parallel graphics stats4 stats utils
[8] methods base
other attached packages:
[1] dplyr_0.8.3 EnhancedVolcano_1.0.1 ggrepel_0.8.1
[4] ggplot2_3.2.1 biomaRt_2.38.0 GenomicRanges_1.34.0
[7] GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1
[10] BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] httr_1.4.1 Biobase_2.42.0
[3] bit64_0.9-7 splines_3.5.2
[5] Formula_1.2-3 assertthat_0.2.1
[7] BiocManager_1.30.4 latticeExtra_0.6-28
[9] blob_1.2.0 GenomeInfoDbData_1.2.0
[11] yaml_2.2.0 progress_1.2.2
[13] pillar_1.4.2 RSQLite_2.1.2
[15] backports_1.1.4 lattice_0.20-38
[17] glue_1.3.1 digest_0.6.20
[19] RColorBrewer_1.1-2 XVector_0.22.0
[21] checkmate_1.9.4 colorspace_1.4-1
[23] htmltools_0.3.6 Matrix_1.2-17
[25] DESeq2_1.22.2 XML_3.98-1.20
[27] pkgconfig_2.0.2 genefilter_1.64.0
[29] zlibbioc_1.28.0 purrr_0.3.2
[31] xtable_1.8-4 scales_1.0.0
[33] BiocParallel_1.16.6 htmlTable_1.13.1
[35] tibble_2.1.3 annotate_1.60.1
[37] withr_2.1.2 SummarizedExperiment_1.12.0
[39] nnet_7.3-12 lazyeval_0.2.2
[41] survival_2.43-3 magrittr_1.5
[43] crayon_1.3.4 evaluate_0.14
[45] memoise_1.1.0 foreign_0.8-71
[47] prettyunits_1.0.2 tools_3.5.2
[49] data.table_1.12.2 hms_0.5.1
[51] matrixStats_0.54.0 stringr_1.4.0
[53] locfit_1.5-9.1 munsell_0.5.0
[55] cluster_2.0.7-1 DelayedArray_0.8.0
[57] AnnotationDbi_1.44.0 packrat_0.5.0
[59] compiler_3.5.2 rlang_0.4.0
[61] grid_3.5.2 RCurl_1.95-4.12
[63] rstudioapi_0.10 htmlwidgets_1.3
[65] rmarkdown_1.15 bitops_1.0-6
[67] base64enc_0.1-3 gtable_0.3.0
[69] DBI_1.0.0 R6_2.4.0
[71] gridExtra_2.3 knitr_1.24
[73] bit_1.1-14 zeallot_0.1.0
[75] Hmisc_4.2-0 stringi_1.4.3
[77] Rcpp_1.0.2 vctrs_0.2.0
[79] geneplotter_1.60.0 rpart_4.1-13
[81] acepack_1.4.1 tidyselect_0.2.5
[83] xfun_0.9
Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.