warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.

Yunuuuu commented 1 year ago

When I used scater::plotColData, there always prompts some annoying message by ggplot2 deprecated arguments size from element_text() and element_rect()

     invisible(lapply(c("sum", "detected", "subse
     ts_Mito_percent"), function(y) {
         res <- scater::plotColData(sce_raw,
             x = "Sample", y = y,
             colour_by = switch(y,
                 sum = "low_lib_size",
                 detected = "low_n_features",
                 subsets_Mito_percent = "high_sub
     sets_Mito_percent"
             ),
             other_fields = "sample_type"
         )
         if (y %in% c("sum", "detected")) res <- 
     res + scale_y_log10()
         qc_plot <- res +
             facet_grid(
                 cols = vars(sample_type),
                 scales = "free_x", space = "free
     _x"
             ) +
             ggtitle(y) + labs(x = NULL, y = NULL
     ) +
             theme(axis.text.x = element_text(ang
     le = 60, hjust = 1))
         ggsave(
             here("figures", "qc", paste0("raw_",
      y, "_qc.pdf")),
             qc_plot,
             device = pdf, width = 12, height = 5

         )
     }))

here is the output:

Warning messages:
1: In y_by_out$val : partial match of 'val' to 'value'
2: In x_by_out$val : partial match of 'val' to 'value'
3: The `size` argument of `element_line()` is
deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the
  cowplot package.
  Please report the issue at
  <https://github.com/wilkelab/cowplot/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to
see where this warning was generated. 
4: The `size` argument of `element_rect()` is
deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the
  cowplot package.
  Please report the issue at
  <https://github.com/wilkelab/cowplot/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to
see where this warning was generated.

My sessionInfo is here:

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so

locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=zh_CN.UTF-8
[12] LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices
[5] utils     datasets  methods   base     

other attached packages:
 [1] here_1.0.1                 
 [2] magrittr_2.0.3             
 [3] ggplot2_3.3.6.9000         
 [4] SingleCellExperiment_1.20.0
 [5] SummarizedExperiment_1.28.0
 [6] Biobase_2.58.0             
 [7] GenomicRanges_1.50.0       
 [8] GenomeInfoDb_1.34.0        
 [9] IRanges_2.32.0             
[10] S4Vectors_0.36.0           
[11] BiocGenerics_0.44.0        
[12] MatrixGenerics_1.10.0      
[13] matrixStats_0.62.0         

loaded via a namespace (and not attached):
 [1] ggrepel_0.9.1            
 [2] Rcpp_1.0.9               
 [3] rsvd_1.0.5               
 [4] lattice_0.20-45          
 [5] pak_0.3.1                
 [6] assertthat_0.2.1         
 [7] rprojroot_2.0.3          
 [8] digest_0.6.30            
 [9] utf8_1.2.2               
[10] R6_2.5.1                 
[11] pillar_1.8.1             
[12] sparseMatrixStats_1.10.0 
[13] zlibbioc_1.44.0          
[14] rlang_1.0.6              
[15] irlba_2.3.5.1            
[16] Matrix_1.5-1             
[17] labeling_0.4.2           
[18] BiocNeighbors_1.16.0     
[19] BiocParallel_1.32.0      
[20] RCurl_1.98-1.9           
[21] munsell_0.5.0            
[22] beachmat_2.14.0          
[23] DelayedArray_0.24.0      
[24] compiler_4.2.1           
[25] vipor_0.4.5              
[26] BiocSingular_1.14.0      
[27] pkgconfig_2.0.3          
[28] ggbeeswarm_0.6.0         
[29] tidyselect_1.2.0         
[30] tibble_3.1.8             
[31] gridExtra_2.3            
[32] GenomeInfoDbData_1.2.9   
[33] progressr_0.11.0         
[34] codetools_0.2-18         
[35] viridisLite_0.4.1        
[36] fansi_1.0.3              
[37] crayon_1.5.2             
[38] dplyr_1.0.10             
[39] withr_2.5.0              
[40] bitops_1.0-7             
[41] grid_4.2.1               
[42] jsonlite_1.8.3           
[43] gtable_0.3.1             
[44] lifecycle_1.0.3.9000     
[45] DBI_1.1.3                
[46] scales_1.2.1             
[47] ScaledMatrix_1.6.0       
[48] cli_3.4.1                
[49] scuttle_1.8.0            
[50] farver_2.1.1             
[51] XVector_0.38.0           
[52] viridis_0.6.2            
[53] scater_1.26.0            
[54] DelayedMatrixStats_1.20.0
[55] generics_0.1.3           
[56] vctrs_0.5.0              
[57] cowplot_1.1.1            
[58] ggsci_2.9                
[59] tools_4.2.1              
[60] glue_1.6.2               
[61] beeswarm_0.4.0           
[62] parallel_4.2.1           
[63] colorspace_2.0-3

clauswilke commented 1 year ago

Thanks for bringing this up. This is caused by a change in the latest released ggplot2. A couple of things to consider for a fix:

The moment this is fixed, cowplot stops working with older versions of ggplot2. So this dependency needs to be recorded in the DESCRIPTION file.
We should make sure we find all occurrences in the code that can cause this problem, so we need to fix only once.

Also, a general comment: When reporting issues, it's most productive to try to come up with a minimal example that causes the problem. Minimal examples should definitely not depend on other packages or have all sorts of irrelevant, distracting code. Here, I believe the problem is caused by using certain cowplot themes, but I can't tell from the provided example.

clauswilke commented 1 year ago

I see you provided a minimal example here: https://github.com/wilkelab/cowplot/pull/189#issuecomment-1305723678

Yunuuuu commented 1 year ago

Oh, I'll put it here

Yunuuuu commented 1 year ago

A minimal example

library(ggplot2)
library(cowplot)

ggplot(mtcars) +
    geom_point(aes(mpg, drat)) +
    theme_cowplot()

Warning messages:
1: The `size` argument of `element_line()` is
deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the
  cowplot package.
  Please report the issue at
  <https://github.com/wilkelab/cowplot/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to
see where this warning was generated. 
2: The `size` argument of `element_rect()` is
deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the
  cowplot package.
  Please report the issue at
  <https://github.com/wilkelab/cowplot/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to
see where this warning was generated.

Yunuuuu commented 1 year ago

fixed by https://github.com/wilkelab/cowplot/pull/189

wilkelab / cowplot

warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. #190