Error: addDoubletScores about ggplot2

[yuyuyuto001]

Hey everybody.

I had an error when I used addDoubletScores function.

**Attach log files
ArchR has built-in logging capabilities for complex functions. A log file (which will appear in the console output) must be attached to this issue. Drag and drop it here.
ArchR-addDoubletScores-1b70395bc576-Date-2024-02-29_Time-09-57-38.155893.log

Bug Description.
When I use the addDoubletScores function, I get the following error.

doubScores <- addDoubletScores(

• input = ArrowFiles,
• k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
• knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search.
• LSIMethod = 1
• )
  ArchR logging to : ArchRLogs/ArchR-addDoubletScores-1b70395bc576-Date-2024-02-29_Time-09-57-38.155893.log
  If there is an issue, please report to github with logFile!
  2024-02-29 09:57:38.221589 : Batch Execution w/ safelapply!, 0 mins elapsed.
  2024-02-29 09:57:38.231848 : scATAC_BMMC_R1 (1 of 3) : Computing Doublet Statistics, 0 mins elapsed.
  Warning: Data is of class matrix. Coercing to dgCMatrix.
  Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
  Also defined by ‘spam’
  Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
  Also defined by ‘spam’
  scATAC_BMMC_R1 (1 of 3) : UMAP Projection R^2 = 0.97882

---

2024-02-29 10:00:00.474936 : ERROR Found in ggplot for scATAC_BMMC_R1 (1 of 3) :
LogFile = ArchRLogs/ArchR-addDoubletScores-1b70395bc576-Date-2024-02-29_Time-09-57-38.155893.log

<simpleError in g$grobs[[legend]]: no such index at level 2

---

2024-02-29 10:00:00.507234 : scATAC_CD34_BMMC_R1 (2 of 3) : Computing Doublet Statistics, 2.371 mins elapsed.
Warning: Data is of class matrix. Coercing to dgCMatrix.
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
scATAC_CD34_BMMC_R1 (2 of 3) : UMAP Projection R^2 = 0.99203

---

2024-02-29 10:01:55.924854 : ERROR Found in ggplot for scATAC_CD34_BMMC_R1 (2 of 3) :
LogFile = ArchRLogs/ArchR-addDoubletScores-1b70395bc576-Date-2024-02-29_Time-09-57-38.155893.log

<simpleError in g$grobs[[legend]]: no such index at level 2

---

2024-02-29 10:01:55.957149 : scATAC_PBMC_R1 (3 of 3) : Computing Doublet Statistics, 4.296 mins elapsed.
Warning: Data is of class matrix. Coercing to dgCMatrix.
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
scATAC_PBMC_R1 (3 of 3) : UMAP Projection R^2 = 0.96012

---

2024-02-29 10:03:56.628193 : ERROR Found in ggplot for scATAC_PBMC_R1 (3 of 3) :
LogFile = ArchRLogs/ArchR-addDoubletScores-1b70395bc576-Date-2024-02-29_Time-09-57-38.155893.log

<simpleError in g$grobs[[legend]]: no such index at level 2

---

ArchR logging successful to : ArchRLogs/ArchR-addDoubletScores-1b70395bc576-Date-2024-02-29_Time-09-57-38.155893.log

**How to reproduce
I can reproduce it with the tutorial dataset, and the above code is tutorial's.

Additional Context.
I reinstalled ArchR and ggplot2, and tried to restart R and R studio several times, but the problem wasn't solved.
Could you help me to solve this error?
Thanks in advance!

[huiqizhu]

I have the same error. Have you solved this?

[nansne]

I encountered this error during call peaking. The call peaking process has been completed, However, I got an error message that says "Error in g$grobs[[legend]]: no such index at level 2". Have you solved this?

[nansne]

I encountered this error during call peaking. The call peaking process has been completed, However, I got an error message that says "Error in g$grobs[[legend]]: no such index at level 2". Have you solved this?

[nansne]

ggplot2 version changed to 3.4.4,not 3.5

[alekseybelikov]

solved ggplot errors by downgrading to version 3.4.0

ggplot_url <- "https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.4.0.tar.gz"
install.packages(ggplot_url, repos=NULL, type="source")