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Version Info

## Warning: replacing previous import 'dplyr::as_data_frame' by
## 'igraph::as_data_frame' when loading 'CrossTalkeR'
## Warning: replacing previous import 'dplyr::groups' by 'igraph::groups' when
## loading 'CrossTalkeR'
## Warning: replacing previous import 'clusterProfiler::simplify' by
## 'igraph::simplify' when loading 'CrossTalkeR'
## Warning: replacing previous import 'dplyr::union' by 'igraph::union' when
## loading 'CrossTalkeR'
## Warning: replacing previous import 'igraph::as_data_frame' by
## 'tibble::as_data_frame' when loading 'CrossTalkeR'
## Warning: replacing previous import 'assertthat::has_name' by 'tibble::has_name'
## when loading 'CrossTalkeR'
## Warning: replacing previous import 'igraph::crossing' by 'tidyr::crossing' when
## loading 'CrossTalkeR'

R version: R version 4.3.2 (2023-10-31)

Package version: 1.4.0

Generate Report Example

In our vignette we provide examples on how to analyse cell interactions from a human myelofibrosis single cell RNA-seq dataset.

paths <- c('CTR' = system.file("extdata",
                               "CTR_LR.csv",
                               package = "CrossTalkeR"),
           'EXP' = system.file("extdata",
                               "EXP_LR.csv",
                               package = "CrossTalkeR"))
genes <- c('TGFB1|L')
output <- system.file("extdata", package = "CrossTalkeR")
data <- generate_report(paths,
                        genes,
                        out_path=paste0(output,'/'),
                        threshold=0,
                        out_file = 'vignettes_example.html',
                        output_fmt = "html_document",
                        report = TRUE)

Individual Visualization

CCI

plot_cci(graph = data@graphs$CTR,
        colors = data@colors,
        plt_name = 'Example 1',
        coords = data@coords[V(data@graphs$CTR)$name,],
        emax = NULL,
        leg = FALSE,
        low = 0,
        high = 0,
        ignore_alpha = FALSE,
        log = FALSE,
        efactor = 8,
        vfactor = 12)

Sankey plot

plot_sankey(lrobj_tbl = data@tables$EXP_x_CTR,
            target = c("TGFB1|L"),
            ligand_cluster = NULL,
            receptor_cluster = NULL,
            plt_name = "TGFB1")

Report Samples

Single

Comparative

Session information

## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Europe/Berlin
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] knitr_1.44            colorBlindness_0.1.9  extrafont_0.19       
##  [4] pals_1.7              graphlayouts_1.0.0    ggrepel_0.9.3        
##  [7] DT_0.28               ComplexHeatmap_2.16.0 factoextra_1.0.7     
## [10] patchwork_1.1.2       stringr_1.5.0         tidyr_1.3.0          
## [13] tibble_3.2.1          dplyr_1.1.2           ggraph_2.1.0         
## [16] ggplot2_3.4.2         igraph_1.5.0.1        CrossTalkeR_1.4.0    
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.3.2           bitops_1.0-7            ggplotify_0.1.1        
##   [4] polyclip_1.10-4         lifecycle_1.0.3         rstatix_0.7.2          
##   [7] doParallel_1.0.17       rprojroot_2.0.3         lattice_0.22-5         
##  [10] MASS_7.3-60             crosstalk_1.2.0         backports_1.4.1        
##  [13] magrittr_2.0.3          sass_0.4.7              rmarkdown_2.23         
##  [16] jquerylib_0.1.4         yaml_2.3.7              mapproj_1.2.11         
##  [19] cowplot_1.1.1           DBI_1.1.3               RColorBrewer_1.1-3     
##  [22] maps_3.4.1              abind_1.4-5             zlibbioc_1.46.0        
##  [25] purrr_1.0.1             BiocGenerics_0.46.0     RCurl_1.98-1.12        
##  [28] yulab.utils_0.0.6       tweenr_2.0.2            circlize_0.4.15        
##  [31] GenomeInfoDbData_1.2.10 IRanges_2.34.1          S4Vectors_0.38.1       
##  [34] enrichplot_1.20.0       tidytree_0.4.4          pkgdown_2.0.7          
##  [37] codetools_0.2-19        DOSE_3.26.1             ggforce_0.4.1          
##  [40] tidyselect_1.2.0        shape_1.4.6             aplot_0.1.10           
##  [43] farver_2.1.1            viridis_0.6.4           matrixStats_1.0.0      
##  [46] stats4_4.3.2            jsonlite_1.8.7          GetoptLong_1.0.5       
##  [49] ellipsis_0.3.2          tidygraph_1.2.3         ggalluvial_0.12.5      
##  [52] iterators_1.0.14        systemfonts_1.0.4       foreach_1.5.2          
##  [55] tools_4.3.2             treeio_1.24.3           ragg_1.2.5             
##  [58] sna_2.7-1               Rcpp_1.0.11             glue_1.6.2             
##  [61] Rttf2pt1_1.3.12         gridExtra_2.3           xfun_0.39              
##  [64] qvalue_2.32.0           GenomeInfoDb_1.36.1     withr_2.5.0            
##  [67] fastmap_1.1.1           boot_1.3-28.1           fansi_1.0.4            
##  [70] SparseM_1.81            digest_0.6.33           networkLite_1.0.5      
##  [73] R6_2.5.1                mime_0.12               gridGraphics_0.5-1     
##  [76] textshaping_0.3.6       colorspace_2.1-0        Cairo_1.6-0            
##  [79] GO.db_3.17.0            dichromat_2.0-0.1       RSQLite_2.3.1          
##  [82] utf8_1.2.3              generics_0.1.3          data.table_1.14.8      
##  [85] httr_1.4.6              htmlwidgets_1.6.2       scatterpie_0.2.1       
##  [88] org.Mm.eg.db_3.17.0     pkgconfig_2.0.3         gtable_0.3.3           
##  [91] blob_1.2.4              networkDynamic_0.11.3   XVector_0.40.0         
##  [94] clusterProfiler_4.8.2   shadowtext_0.1.2        htmltools_0.5.5        
##  [97] carData_3.0-5           fgsea_1.26.0            clue_0.3-64            
## [100] scales_1.2.1            Biobase_2.60.0          png_0.1-8              
## [103] ggfun_0.1.1             reshape2_1.4.4          rjson_0.2.21           
## [106] coda_0.19-4             statnet.common_4.9.0    nlme_3.1-163           
## [109] org.Hs.eg.db_3.17.0     cachem_1.0.8            GlobalOptions_0.1.2    
## [112] parallel_4.3.2          HDO.db_0.99.1           AnnotationDbi_1.62.2   
## [115] desc_1.4.2              pillar_1.9.0            vctrs_0.6.3            
## [118] ggpubr_0.6.0            car_3.1-2               cluster_2.1.6          
## [121] extrafontdb_1.0         netdiffuseR_1.22.5      evaluate_0.21          
## [124] magick_2.7.5            cli_3.6.1               compiler_4.3.2         
## [127] rlang_1.1.1             crayon_1.5.2            MatchIt_4.5.4          
## [130] ggsignif_0.6.4          labeling_0.4.2          plyr_1.8.8             
## [133] fs_1.6.3                stringi_1.7.12          viridisLite_0.4.2      
## [136] network_1.18.1          BiocParallel_1.34.2     assertthat_0.2.1       
## [139] munsell_0.5.0           Biostrings_2.68.1       lazyeval_0.2.2         
## [142] GOSemSim_2.26.1         Matrix_1.5-1            bit64_4.0.5            
## [145] KEGGREST_1.40.0         gsw_1.1-1               broom_1.0.5            
## [148] memoise_2.0.1           oce_1.8-1               bslib_0.5.0            
## [151] ggtree_3.8.2            fastmatch_1.1-3         bit_4.0.5              
## [154] downloader_0.4          ape_5.7-1               gson_0.1.0