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kuwisdelu / Cardinal

Mass spectrometry imaging toolbox
http://www.cardinalmsi.org
Artistic License 2.0
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error in image when all intensity values are equal #12

Closed NHPatterson closed 6 months ago

NHPatterson commented 4 years ago

I was recently plotting some binary masks and found this potential bug when plotting a binary mask where all values are equal. Seems to be more related to image.default than Cardinal itself but it could be an issue for someone else at some point.

Minimal reproducible example...

xy <- expand.grid(x=c(1:5),y=c(1:5))
ms_data <- matrix(1, ncol=nrow(xy),nrow=1)

cdata <- MSImagingExperiment(
  imageData = ms_data,
  featureData = MassDataFrame(mz = 1),
  pixelData = PositionDataFrame(coord=xy, run = "binary_test"),
  centroided = T)

image(cdata, mz=1)

returns a plot with an error:

Error in image.default(1, vals, t(as.matrix(vals)), col = col, xaxt = "n",  : 
  increasing 'x' and 'y' values expected

notworking

Minimal working example...

xy <- expand.grid(x=c(1:5),y=c(1:5))
ms_data_rand <- matrix(rnorm(nrow(xy),mean=0,sd=1), ncol=nrow(xy),nrow=1)

cdata_randint <- MSImagingExperiment(
  imageData = ms_data_rand,
  featureData = MassDataFrame(mz = 1),
  pixelData = PositionDataFrame(coord=xy, run = "rand_test"),
  centroided = T)

image(cdata_randint, mz=1)

working

No error here.

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] Cardinal_2.6.0      ProtGenerics_1.20.0 S4Vectors_0.26.1    EBImage_4.30.0     
[5] BiocParallel_1.22.0 BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6      compiler_4.0.0    pillar_1.4.4      matter_1.14.0    
 [5] bitops_1.0-6      tools_4.0.0       mclust_5.4.6      digest_0.6.25    
 [9] viridisLite_0.3.0 lifecycle_0.2.0   tibble_3.0.1      nlme_3.1-147     
[13] lattice_0.20-41   pkgconfig_2.0.3   png_0.1-7         rlang_0.4.6      
[17] Matrix_1.2-18     DBI_1.1.0         biglm_0.9-2       dplyr_1.0.0      
[21] generics_0.0.2    fftwtools_0.9-8   htmlwidgets_1.5.1 vctrs_0.3.0      
[25] locfit_1.5-9.4    grid_4.0.0        tidyselect_1.1.0  glue_1.4.1       
[29] Biobase_2.48.0    R6_2.4.1          jpeg_0.1-8.1      sp_1.4-2         
[33] irlba_2.3.3       purrr_0.3.4       magrittr_1.5      MASS_7.3-51.6    
[37] htmltools_0.4.0   ellipsis_0.3.1    abind_1.4-5       tiff_0.1-5       
[41] signal_0.7-6      RCurl_1.98-1.2    crayon_1.3.4