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Shians / Glimma

Glimma R package
GNU Lesser General Public License v3.0
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glimmaMDS/glimmaMD can't find local directories #177

Open jdrnevich opened 3 years ago

jdrnevich commented 3 years ago

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 3 years ago

Update: "The system cannot find the file specified" only happens on Windows. All the above work fine on Mac. Haven't tested Linux.