Error from plotting sce object: '.abundance_counts' not found #92
Description
Hi there,
I have an sce object obtained after doing CATALYST clustering of the flow cytometry data, and I want to use tidySingleCellExperiement package to manipulate the object.
I was trying to plot some channels/markers as below, but unsure which data the function .abundance_counts is drawing from, given the error below.
Would you mind giving me some pointer?
Thank you.
> F37_sce_backboneClustering
# A SingleCellExperiment-tibble abstraction: 4,955,453 × 17
# Features=270 | Assays=exprs
.cell sample_id cell_count_prePeacoQC cell_count_postPeacoQC manualInspect_strang…¹
<chr> <fct> <fct> <fct> <fct>
1 CATALYST28meta16_12_1 F37_10D_CD4… 50819 50785 Expected
2 CATALYST28meta16_3_2 F37_10D_CD4… 50819 50785 Expected
3 CATALYST28meta16_3_3 F37_10D_CD4… 50819 50785 Expected
4 CATALYST28meta16_2_4 F37_10D_CD4… 50819 50785 Expected
5 CATALYST28meta16_3_5 F37_10D_CD4… 50819 50785 Expected
6 CATALYST28meta16_2_6 F37_10D_CD4… 50819 50785 Expected
7 CATALYST28meta16_8_7 F37_10D_CD4… 50819 50785 Expected
8 CATALYST28meta16_3_8 F37_10D_CD4… 50819 50785 Expected
9 CATALYST28meta16_3_9 F37_10D_CD4… 50819 50785 Expected
10 CATALYST28meta16_3_10 F37_10D_CD4… 50819 50785 Expected
# ℹ 4,955,443 more rows
# ℹ abbreviated name: ¹manualInspect_strangeFCS
# ℹ 12 more variables: preFilter_liveCD3CD8_count <fct>, flowJo_prePeacoQC_gMFI_PE <fct>,
# flowCore_postPeacoQC_medMFI_PE <fct>, cluster_id <fct>, CATALYST28meta16 <fct>, nColID <fct>,
# CATALYST28meta16_nColID <chr>, CATALYST28meta16_uniqueLetterID <fct>, UMAP1 <dbl>, UMAP2 <dbl>,
# TSNE1 <dbl>, TSNE2 <dbl>
# ℹ Use `print(n = ...)` to see more rows
> F37_sce_backboneClustering |>
+ join_features(features=c("CD4", "CD8")) |>
+ ggplot(aes(CATALYST28meta16, .abundance_counts + 1, fill=CATALYST28meta16)) +
+ geom_boxplot(outlier.shape=NA) +
+ scale_y_log10() +
+ custom_theme
tidySingleCellExperiment says: This operation lead to duplicated cell names. A data frame is returned for independent data analysis.
Error in `geom_boxplot()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `FUN()`:
! object '.abundance_counts' not found
Backtrace:
1. base (local) `<fn>`(x)
2. ggplot2:::print.ggplot(x)
4. ggplot2:::ggplot_build.ggplot(x)
5. ggplot2:::by_layer(...)
12. ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. l$compute_aesthetics(d, plot)
14. ggplot2 (local) compute_aesthetics(..., self = self)
15. base::lapply(aesthetics, eval_tidy, data = data, env = env)
16. rlang (local) FUN(X[[i]], ...)