plot_measure_dim error
WesAus10 opened this issue · comments
Hi, I recently found your package and love it but I ran into an error when trying to call plot_measure_dim. Example below uses the tutorial data.
> plot_measure_dim(dataset = scRNA_int,
+ measures = c("nFeature_RNA","nCount_RNA","percent.mt","KRT14"))
Error in `plot_measure_dim()`:
! Can't subset `.data` outside of a data mask context.
Run `rlang::last_error()` to see where the error occurred.
> rlang::last_error()
<error/rlang_error>
Error in `plot_measure_dim()`:
! Can't subset `.data` outside of a data mask context.
---
Backtrace:
1. Scillus::plot_measure_dim(...)
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/rlang_error>
Error in `plot_measure_dim()`:
! Can't subset `.data` outside of a data mask context.
---
Backtrace:
▆
1. └─**Scillus**::plot_measure_dim(...)
2. ├─ggplot2::scale_color_viridis_c(...)
3. │ └─ggplot2::continuous_scale(...)
4. ├─**stats**::quantile(.data[[measures[i]]], probs = 0.1)
5. ├─<unknown>
6. └─**rlang**:::`[[.rlang_fake_data_pronoun`(.data, measures[i])
7. └─rlang:::stop_fake_data_subset(call)
8. └─rlang::abort(...)
Here's my sessionInfo
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_2.0.3 SeuratObject_4.0.4 Seurat_4.1.0 forcats_0.5.1
[5] stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4 readr_2.1.2
[9] tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
[13] Scillus_0.5.0
loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 circlize_0.4.14
[4] plyr_1.8.7 igraph_1.3.0 lazyeval_0.2.2
[7] splines_4.1.3 listenv_0.8.0 scattermore_0.8
[10] digest_0.6.29 foreach_1.5.2 htmltools_0.5.2
[13] formattable_0.2.1 fansi_1.0.3 tensor_1.5
[16] cluster_2.1.3 doParallel_1.0.17 ROCR_1.0-11
[19] tzdb_0.3.0 ComplexHeatmap_2.10.0 globals_0.14.0
[22] modelr_0.1.8 matrixStats_0.61.0 R.utils_2.11.0
[25] spatstat.sparse_2.1-0 colorspace_2.0-3 rvest_1.0.2
[28] ggrepel_0.9.1 haven_2.4.3 xfun_0.30
[31] crayon_1.5.1 jsonlite_1.8.0 spatstat.data_2.1-4
[34] survival_3.3-1 zoo_1.8-9 iterators_1.0.14
[37] glue_1.6.2 polyclip_1.10-0 gtable_0.3.0
[40] leiden_0.3.9 GetoptLong_1.0.5 future.apply_1.8.1
[43] shape_1.4.6 BiocGenerics_0.40.0 abind_1.4-5
[46] scales_1.1.1 DBI_1.1.2 spatstat.random_2.2-0
[49] miniUI_0.1.1.1 Rcpp_1.0.8.3 viridisLite_0.4.0
[52] xtable_1.8-4 clue_0.3-60 reticulate_1.24
[55] spatstat.core_2.4-2 stats4_4.1.3 htmlwidgets_1.5.4
[58] httr_1.4.2 RColorBrewer_1.1-3 ellipsis_0.3.2
[61] ica_1.0-2 farver_2.1.0 R.methodsS3_1.8.1
[64] pkgconfig_2.0.3 uwot_0.1.11 dbplyr_2.1.1
[67] deldir_1.0-6 utf8_1.2.2 labeling_0.4.2
[70] tidyselect_1.1.2 rlang_1.0.2 reshape2_1.4.4
[73] later_1.3.0 cellranger_1.1.0 munsell_0.5.0
[76] tools_4.1.3 cli_3.2.0 generics_0.1.2
[79] broom_0.8.0 ggridges_0.5.3 evaluate_0.15
[82] fastmap_1.1.0 goftest_1.2-3 fs_1.5.2
[85] knitr_1.38 fitdistrplus_1.1-8 RANN_2.6.1
[88] pbapply_1.5-0 future_1.24.0 nlme_3.1-157
[91] mime_0.12 R.oo_1.24.0 xml2_1.3.3
[94] rstudioapi_0.13 compiler_4.1.3 plotly_4.10.0
[97] png_0.1-7 spatstat.utils_2.3-0 reprex_2.0.1
[100] stringi_1.7.6 RSpectra_0.16-0 lattice_0.20-45
[103] Matrix_1.4-1 vctrs_0.4.1 pillar_1.7.0
[106] lifecycle_1.0.1 spatstat.geom_2.4-0 lmtest_0.9-40
[109] GlobalOptions_0.1.2 RcppAnnoy_0.0.19 data.table_1.14.2
[112] cowplot_1.1.1 irlba_2.3.5 httpuv_1.6.5
[115] patchwork_1.1.1 R6_2.5.1 promises_1.2.0.1
[118] KernSmooth_2.23-20 gridExtra_2.3 IRanges_2.28.0
[121] parallelly_1.31.0 codetools_0.2-18 MASS_7.3-56
[124] assertthat_0.2.1 rjson_0.2.21 withr_2.5.0
[127] sctransform_0.3.3 S4Vectors_0.32.4 mgcv_1.8-40
[130] parallel_4.1.3 hms_1.1.1 grid_4.1.3
[133] rpart_4.1.16 rmarkdown_2.13 Rtsne_0.15
[136] shiny_1.7.1 lubridate_1.8.0
The same mistake!
Excuse me, has this problem been solved? Is there any technician who can help to solve it?
ISSUE SOLVED @WesAus10 @yaqi2731
I got this error too. I tried to change every .data to df in the source code of the function plot_measure_dim()
Fortunately, it works!!! But I don't understand why...
You could build a new function (e.g. plot_measure_dim2) by yourselves:
plot_measure_dim2 <- function (dataset, measures, split_by = NA, point.size = 1)
{
l <- get_measure_data(dataset = dataset, measures = measures,
return_df = FALSE)
split_by <- ifelse(split_by == "No Split", NA, split_by)
df <- l[[1]]
measures <- l[[2]]
p <- list()
for (i in seq_along(1:length(measures))) {
p[[i]] <- ggplot(df) + geom_point(aes(x = UMAP_1,
y = UMAP_2, color = df[[measures[i]]]),
size = point.size) + scale_color_viridis_c(option = "A",
name = "", direction = -1, limits = c(quantile(df[[measures[i]]],
probs = 0.1), quantile(df[[measures[i]]],
probs = 0.9)), oob = scales::squish) + theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), panel.background = element_blank(),
axis.text = element_text(size = 12), axis.title = element_text(size = 12),
panel.border = element_rect(colour = "black", fill = NA,
linewidth = 1, linetype = 1), axis.line = element_blank()) +
labs(x = "UMAP_1", y = "UMAP_2") + ggtitle(measures[i]) +
if (!is.na(split_by)) {
facet_wrap(as.formula(paste("~", split_by)))
}
else {
theme(aspect.ratio = 1)
}
}
patchwork::wrap_plots(p)
}