error message during runScAnnotation process "runCellInteraction"

[wulc21]

Dear professor, when I run runScAnnotation function,I encounter the error message as follows, can you help me to solve the problem, thank you very much.

rm(list=ls()) library(scCancer) setwd("Desktop/scRNA/scCancer/") dataPath <-"./data/KC-example/" statPath <- "./results/KC-example/" savePath <- "./results/KC-example/" sampleName <- "sample1" # The sample name authorName <- "Xiaobei" anno.results <- runScAnnotation(

• dataPath = dataPath,
• statPath = statPath,
• savePath = savePath,
• authorName = authorName,
• sampleName = sampleName,
• geneSet.method = "average" # or "GSVA"
• ) [2021-09-01 17:56:36] START: RUN scAnnotation [2021-09-01 17:56:36] -----: data preparation [2021-09-01 17:57:11] -----: Seurat object creation [2021-09-01 17:57:12] -----: highly variable genes [2021-09-01 17:57:14] -----: data scaling [2021-09-01 17:57:41] -----: PCA [2021-09-01 17:57:52] -----: clustering [2021-09-01 17:57:56] -----: tSNE [2021-09-01 17:58:27] -----: UMAP [2021-09-01 17:58:45] -----: differential expression analysis [2021-09-01 18:00:11] -----: Seurat plotting and saving When using repel, set xnudge and ynudge to 0 for optimal results [2021-09-01 18:00:34] -----: Doublet score estimation [18:01:37] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior. [2021-09-01 18:01:45] -----: TME cell types annotation [2021-09-01 18:05:27] -----: cells malignancy annotation [2021-09-01 18:12:14] -----: cell cycle score estimation [2021-09-01 18:12:15] -----: stemness score calculation [2021-09-01 18:12:20] -----: gene set signatures analysis [2021-09-01 18:12:58] -----: expression programs analysis ### [2021-09-01 18:21:03] -----: cell interaction analysis Error in UseMethod("depth") : "depth"没有适用于"NULL"目标对象的方法 此外: Warning message: Transformation introduced infinite values in continuous x-axis

[wulc21]

Well, I have solved the problem by use the following code in Terminal

"pip install xgboost==1.2.0"

based on the Warning Message:WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.

after that I restart R and retried the runScAnnotation code and got it.

anno.results <- runScAnnotation(

• dataPath = dataPath,
• statPath = statPath,
• savePath = savePath,
• authorName = authorName,
• sampleName = sampleName,
• geneSet.method = "average" # or "GSVA"
• ) [2021-09-01 19:04:53] START: RUN scAnnotation [2021-09-01 19:04:53] -----: data preparation 2021-09-01 19:05:04.996 R[4345:933983] IMKClient Stall detected, please Report your user scenario attaching a spindump (or sysdiagnose) that captures the problem - (imkxpc_bundleIdentifierWithReply:) block performed very slowly (1.27 secs). [2021-09-01 19:05:31] -----: Seurat object creation [2021-09-01 19:05:32] -----: highly variable genes [2021-09-01 19:05:34] -----: data scaling [2021-09-01 19:06:02] -----: PCA [2021-09-01 19:06:14] -----: clustering [2021-09-01 19:06:17] -----: tSNE [2021-09-01 19:06:48] -----: UMAP [2021-09-01 19:07:06] -----: differential expression analysis [2021-09-01 19:08:34] -----: Seurat plotting and saving When using repel, set xnudge and ynudge to 0 for optimal results [2021-09-01 19:08:58] -----: Doublet score estimation [19:10:01] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior. [2021-09-01 19:10:09] -----: TME cell types annotation [2021-09-01 19:13:48] -----: cells malignancy annotation [2021-09-01 19:20:25] -----: cell cycle score estimation [2021-09-01 19:20:26] -----: stemness score calculation [2021-09-01 19:20:31] -----: gene set signatures analysis [2021-09-01 19:21:15] -----: expression programs analysis [2021-09-01 19:29:25] -----: report generating

Warning message: Transformation introduced infinite values in continuous x-axis

However, in this process the warning message sill exist, so why? is it normal? thank you very much.

[wguo-research]

Thanks for your use. The warning message is normal, which is due to that when plotting under log-scale, zero will be transformed to infinite values. It doesn't affect the result.