su: ignoring --preserve-environment, it's mutually exclusive with --login Attaching package: ‘DT’ The following objects are masked from ‘package:shiny’: dataTableOutput, renderDataTable Attaching package: ‘bs4Dash’ The following objects are masked from ‘package:shiny’: actionButton, column, insertTab, navbarMenu, tabsetPanel The following object is masked from ‘package:graphics’: box Attaching package: ‘shinyWidgets’ The following object is masked from ‘package:bs4Dash’: progressBar Attaching package: ‘zip’ The following objects are masked from ‘package:utils’: unzip, zip Loading required package: DBI Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Attaching package: ‘dbplyr’ The following objects are masked from ‘package:dplyr’: ident, sql ========================================================================== IOBR v2.2.0.9000 Immuno-Oncology Biological Research For Documentation: https://iobr.github.io/IOBR/ For Tutorial: https://iobr.github.io/book/ For Help: https://github.com/IOBR/IOBR/issues If you use IOBR in published research, please cite: DQ Zeng, YR Fang, ..., GC Yu*, WJ Liao*, Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0. Cell Rep Methods 4, 100910 (2024). & YR Fang, ..., WJ Liao*, DQ Zeng*, Systematic Investigation of Tumor Microenvironment and Antitumor Immunity With IOBR, Med Research (2025). https://onlinelibrary.wiley.com/doi/epdf/10.1002/mdr2.70001 ========================================================================== IOBRportal database mode: enabled. Listening on http://127.0.0.1:35451 ℹ Trying mirror 1/4: trying URL 'https://github.com/IOBR/IOBR/releases/download/data-v1.0/anno_grch38.rda' Content type 'application/octet-stream' length 1651420 bytes (1.6 MB) ================================================== downloaded 1.6 MB ✔ Download complete: "anno_grch38" ℹ Using local annotation (anno_grch38) for TPM conversion ! Omitting 3985 genes without length information ℹ Found 1679 duplicate symbols. Using "mean" for ranking. ✔ Reduced to 54658 unique genes ✔ Applied log2 transformation ℹ When yinter = -3 ℹ Potential outliers: ℹ Calculating signature scores using ssGSEA method ℹ Log2 transformation not necessary (data appears to already be log-scaled) ℹ Calculating scores for 166 signature(s) ℹ GSVA version 2.4.9 ℹ Searching for rows with constant values ℹ Calculating ssGSEA scores for 165 gene sets ℹ Calculating ranks ℹ Calculating rank weights ℹ Normalizing ssGSEA scores ✔ Calculations finished ℹ Best number of TME clusters: 4 ℹ Cluster distribution: ℹ Creating heatmap with 173 features tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling tidyHeatmap says: If you use tidyHeatmap for scientific research, please cite: Mangiola, S. and Papenfuss, A.T., 2020. 'tidyHeatmap: an R package for modular heatmap production based on tidy principles.' Journal of Open Source Software. doi:10.21105/joss.02472. This message is displayed once per session. Warning: `when()` was deprecated in purrr 1.0.0. ℹ Please use `if` instead. ℹ The deprecated feature was likely used in the tidyHeatmap package. Please report the issue at . ℹ Creating heatmap with 173 features Warning: 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 IOBR package. Please report the issue at . # A tibble: 4 × 5 # Groups: EBV [2] EBV cluster Freq Prop count 1 Negitive TME1 2 0.4 5 2 Negitive TME3 3 0.6 5 3 Positive TME2 2 0.4 5 4 Positive TME4 3 0.6 5 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' # A tibble: 5 × 5 # Groups: EBV [2] EBV stage Freq Prop count 1 Negitive Stage_II 2 0.4 5 2 Negitive Stage_III 3 0.6 5 3 Positive Stage_II 1 0.2 5 4 Positive Stage_III 3 0.6 5 5 Positive Stage_IV 1 0.2 5 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' # A tibble: 5 × 5 # Groups: EBV [2] EBV stage Freq Prop count 1 Negitive Stage_II 2 0.4 5 2 Negitive Stage_III 3 0.6 5 3 Positive Stage_II 1 0.2 5 4 Positive Stage_III 3 0.6 5 5 Positive Stage_IV 1 0.2 5 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' # A tibble: 5 × 5 # Groups: EBV [2] EBV stage Freq Prop count 1 Negitive Stage_II 2 0.4 5 2 Negitive Stage_III 3 0.6 5 3 Positive Stage_II 1 0.2 5 4 Positive Stage_III 3 0.6 5 5 Positive Stage_IV 1 0.2 5 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' # A tibble: 5 × 5 # Groups: EBV [2] EBV stage Freq Prop count 1 Negitive Stage_II 2 0.4 5 2 Negitive Stage_III 3 0.6 5 3 Positive Stage_II 1 0.2 5 4 Positive Stage_III 3 0.6 5 5 Positive Stage_IV 1 0.2 5 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' ℹ Groups: "EBV" and "GS" ℹ Features: 171 ✔ Wilcoxon test complete ℹ Creating heatmap with 20 features ℹ Groups: 2 ("Positive" and "Negitive") ℹ Features: 171 ✔ Kruskal-Wallis test complete ℹ Creating heatmap with 20 features ℹ Showing top 10 signatures `height` was translated to `width`. Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp `height` was translated to `width`. ℹ Best number of TME clusters: 3 ℹ Cluster distribution: ℹ Creating heatmap with 185 features Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'TGFβ_myCAF' in 'mbcsToSbcs': for β (U+03B2) Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'IFNγ_iCAF' in 'mbcsToSbcs': for γ (U+03B3) Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp # A tibble: 11 × 5 # Groups: Stage [5] Stage Cluster Freq Prop count 1 Stage I TME1 5 0.56 9 2 Stage I TME2 2 0.22 9 3 Stage I TME3 2 0.22 9 4 Stage II TME1 29 0.78 37 5 Stage II TME2 8 0.22 37 6 Stage III TME1 13 0.81 16 7 Stage III TME2 2 0.12 16 8 Stage III TME3 1 0.06 16 9 Stage IV TME1 13 0.87 15 10 Stage IV TME3 2 0.13 15 11 TME1 2 1 2 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' ℹ Groups: 4 ("Stage III", "Stage II", "Stage IV", and "Stage I") ℹ Features: 183 ✔ Kruskal-Wallis test complete ℹ Creating heatmap with 20 features ℹ Showing top 10 signatures `height` was translated to `width`. Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp ℹ Survival follow-up time range: 4.11 to 153.72 months ℹ Best cutoff for "CellCycle_Reg": 0.61 ✔ Best cutoff for "CellCycle_Reg": 0.606 ℹ High CellCycle_Reg: 36 ℹ Low CellCycle_Reg: 43 ℹ Maximum follow-up time is 153.7 months; divided into 6 sections Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. ℹ The deprecated feature was likely used in the ggpubr package. Please report the issue at . ℹ Survival follow-up time range: 4.11 to 153.72 months ℹ Best cutoff for "CellCycle_Reg": 0.61 ✔ Best cutoff for "CellCycle_Reg": 0.606 ℹ High CellCycle_Reg: 36 ℹ Low CellCycle_Reg: 43 ℹ Maximum follow-up time is 153.7 months; divided into 6 sections ℹ Survival follow-up time range: 4.11 to 153.72 months ℹ Best cutoff for "CellCycle_Reg": 0.61 ✔ Best cutoff for "CellCycle_Reg": 0.606 ℹ High CellCycle_Reg: 36 ℹ Low CellCycle_Reg: 43 ℹ Maximum follow-up time is 153.7 months; divided into 6 sections ℹ Survival follow-up time range: 4.11 to 153.72 months ℹ Best cutoff for "CellCycle_Reg": 0.61 ✔ Best cutoff for "CellCycle_Reg": 0.606 ℹ High CellCycle_Reg: 36 ℹ Low CellCycle_Reg: 43 ℹ Maximum follow-up time is 153.7 months; divided into 6 sections ℹ Survival follow-up time range: 4.11 to 153.72 months ℹ Best cutoff for "CellCycle_Reg": 0.61 ✔ Best cutoff for "CellCycle_Reg": 0.606 ℹ High CellCycle_Reg: 36 ℹ Low CellCycle_Reg: 43 ℹ Maximum follow-up time is 153.7 months; divided into 6 sections ℹ Follow-up time ranges from 4.11 to 153.72 months Female Male 48 31 ℹ Maximum follow-up time is 153.7 months; divided into 6 sections ℹ Reference group not defined, using alphabetical order ℹ Time range: 4.11 to 153.72 ℹ Input data preview: Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Warning in roc.test.roc(roc1, roc2, method = method, ...) : Progress bars are deprecated in pROC 1.19. Ignoring 'progress' argument ℹ Computing spearman correlation for 184 features Warning in cor.test.default(data[[feat]], data[[target]], method = method, : Cannot compute exact p-value with ties Warning in cor.test.default(data[[feat]], data[[target]], method = method, : Cannot compute exact p-value with ties Warning in cor.test.default(data[[feat]], data[[target]], method = method, : Cannot compute exact p-value with ties ✔ Correlation analysis complete ℹ Calculating spearman correlation (n = 79) ℹ Exact p-value: 9.7e-04 ℹ Calculating pearson correlation: 2 x 2 Closed TCGA pool. Closed OtherCohort pool. Closed Immunotherapy pool. Closed CancerCohort pool. Execution halted