glimmaMDS/glimmaMD can't find local directories
Opened this issue · 1 comments
jdrnevich commented
I'm not sure when you added glimmaMDS and glimmaMD but I just learned about them and I'm super happy to have a stand-alone html version - thanks so much!! I haven't tried to embed them in .Rmd yet, but I did find a bug already: glMDSPlot/glMDPlot had a folder = argument that I used frequently. I can't find that glimmaMDS/glimmaMD have anything like folder = and when I use html = to point to a local subfolder, they cannot find it. Tilda expansion and full path do work inside html =. Example below using your Glimma-limma vignette:
> ## -----------------------------------------------------------------------------
> library(Glimma)
> library(limma)
> library(edgeR)
>
> dge <- readRDS(system.file("RNAseq123/dge.rds", package = "Glimma"))
>
> ## -----------------------------------------------------------------------------
> glimmaMDS(dge, html = "MDS.html")
Saving widget...
MDS.html generated.
>
> dir.create("test")
Warning message:
In dir.create("test") : 'test' already exists
> glimmaMDS(dge, html = "test/MDS.html")
Saving widget...
Error in normalizePath(path.expand(path), winslash, mustWork) :
path[1]="test": The system cannot find the file specified
> glimmaMDS(dge, html = "./test/MDS.html")
Saving widget...
Error in normalizePath(path.expand(path), winslash, mustWork) :
path[1]="./test": The system cannot find the file specified
> glimmaMDS(dge, html = "~/test/MDS.html")
Saving widget...
~/test/MDS.html generated.
> glimmaMDS(dge, html = paste0(getwd(),"/test/MDS.html"))
Saving widget...
C:/GitHubRepos/RNA-Seq/test/MDS.html generated.
>
>
> ## -----------------------------------------------------------------------------
> design <- readRDS(
+ system.file("RNAseq123/design.rds", package = "Glimma"))
> contr.matrix <- readRDS(
+ system.file("RNAseq123/contr.matrix.rds", package = "Glimma"))
>
> ## -----------------------------------------------------------------------------
> v <- voom(dge, design)
> vfit <- lmFit(v, design)
> vfit <- contrasts.fit(vfit, contrasts = contr.matrix)
> efit <- eBayes(vfit)
>
> ## -----------------------------------------------------------------------------
> dge <- estimateDisp(dge, design)
> gfit <- glmFit(dge, design)
> glrt <- glmLRT(gfit, design, contrast = contr.matrix)
>
> ## -----------------------------------------------------------------------------
> glimmaMA(efit, dge = dge, html = "MA.html")
Saving widget...
MA.html generated.
> glimmaMA(efit, dge = dge, html = "test/MA.html")
Saving widget...
Error in normalizePath(path.expand(path), winslash, mustWork) :
path[1]="test": The system cannot find the file specified
> glimmaMA(efit, dge = dge, html = paste0(getwd(), "/test/MA.html"))
Saving widget...
C:/GitHubRepos/RNA-Seq/test/MA.html generated.
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.32.0 limma_3.46.0 Glimma_2.0.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 locfit_1.5-9.4 lattice_0.20-41
[4] digest_0.6.27 R6_2.5.0 GenomeInfoDb_1.26.1
[7] stats4_4.0.3 RSQLite_2.2.1 httr_1.4.2
[10] ggplot2_3.3.2 pillar_1.4.7 zlibbioc_1.36.0
[13] rlang_0.4.9 rstudioapi_0.13 annotate_1.68.0
[16] blob_1.2.1 S4Vectors_0.28.0 Matrix_1.2-18
[19] splines_4.0.3 BiocParallel_1.24.1 geneplotter_1.68.0
[22] htmlwidgets_1.5.2 RCurl_1.98-1.2 bit_4.0.4
[25] munsell_0.5.0 tinytex_0.27 DelayedArray_0.16.0
[28] compiler_4.0.3 xfun_0.19 pkgconfig_2.0.3
[31] BiocGenerics_0.36.0 htmltools_0.5.1.1 tidyselect_1.1.0
[34] SummarizedExperiment_1.20.0 tibble_3.0.4 GenomeInfoDbData_1.2.4
[37] IRanges_2.24.0 matrixStats_0.57.0 XML_3.99-0.5
[40] crayon_1.3.4 dplyr_1.0.2 bitops_1.0-6
[43] grid_4.0.3 jsonlite_1.7.1 xtable_1.8-4
[46] gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0
[49] magrittr_2.0.1 scales_1.1.1 XVector_0.30.0
[52] genefilter_1.72.0 ellipsis_0.3.1 vctrs_0.3.5
[55] generics_0.1.0 RColorBrewer_1.1-2 tools_4.0.3
[58] bit64_4.0.5 Biobase_2.50.0 glue_1.4.2
[61] DESeq2_1.30.0 purrr_0.3.4 MatrixGenerics_1.2.0
[64] yaml_2.2.1 parallel_4.0.3 survival_3.2-7
[67] AnnotationDbi_1.52.0 colorspace_2.0-0 GenomicRanges_1.42.0
[70] memoise_1.1.0
jdrnevich commented
Update: "The system cannot find the file specified" only happens on Windows. All the above work fine on Mac. Haven't tested Linux.