CellChatPlot creates various visualizations for CellChat analysis results stored in a Seurat object.
Usage
CellChatPlot(
srt,
plot_type = "aggregate",
condition = NULL,
pathway = NULL,
dirpath = NULL,
output_format = "pdf",
top_n = 10,
base_height = 1,
base_width = 1,
res = 300,
verbose = TRUE
)Arguments
- srt
A Seurat object that has been processed with RunCellChat.
- plot_type
Type of plot to create. Options:
"aggregate","pathway","comparison","heatmap","circle","bubble","gene".- condition
Condition to plot (if multiple conditions exist).
- pathway
Specific pathway to visualize (for pathway, bubble, and gene plots). If
NULL, uses top pathways.- dirpath
Directory to save plots.
- output_format
Format of output figure:
"png"or"pdf". Default:"png".- top_n
Number of top pathways to use for plotting. Default: 10.
- base_height
Base height multiplier for all plots. Default: 1.
- base_width
Base width multiplier for all plots. Default: 1.
- res
Resolution for PNG output. Default: 300.
- verbose
Whether to print the message. Default is
TRUE.
Examples
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2025-11-13 11:35:03] Start standard scop workflow...
#> ℹ [2025-11-13 11:35:05] Checking a list of <Seurat> object...
#> ! [2025-11-13 11:35:05] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2025-11-13 11:35:05] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2025-11-13 11:35:07] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2025-11-13 11:35:08] Use the separate HVF from srt_list
#> ℹ [2025-11-13 11:35:08] Number of available HVF: 2000
#> ℹ [2025-11-13 11:35:08] Finished check
#> ℹ [2025-11-13 11:35:09] Perform `Seurat::ScaleData()`
#> Warning: Different features in new layer data than already exists for scale.data
#> ℹ [2025-11-13 11:35:10] Perform pca linear dimension reduction
#> StandardPC_ 1
#> Positive: Aplp1, Cpe, Gnas, Fam183b, Map1b, Hmgn3, Pcsk1n, Chga, Tuba1a, Bex2
#> Syt13, Isl1, 1700086L19Rik, Pax6, Chgb, Scgn, Rbp4, Scg3, Gch1, Camk2n1
#> Cryba2, Pcsk2, Pyy, Tspan7, Mafb, Hist3h2ba, Dbpht2, Abcc8, Rap1b, Slc38a5
#> Negative: Spp1, Anxa2, Sparc, Dbi, 1700011H14Rik, Wfdc2, Gsta3, Adamts1, Clu, Mgst1
#> Bicc1, Ldha, Vim, Cldn3, Cyr61, Rps2, Mt1, Ptn, Phgdh, Nudt19
#> Smtnl2, Smco4, Habp2, Mt2, Col18a1, Rpl12, Galk1, Cldn10, Acot1, Ccnd1
#> StandardPC_ 2
#> Positive: Rbp4, Tagln2, Tuba1b, Fkbp2, Pyy, Pcsk2, Iapp, Tmem27, Meis2, Tubb4b
#> Pcsk1n, Dbpht2, Rap1b, Dynll1, Tubb2a, Sdf2l1, Scgn, 1700086L19Rik, Scg2, Abcc8
#> Atp1b1, Hspa5, Fam183b, Papss2, Slc38a5, Scg3, Mageh1, Tspan7, Ppp1r1a, Ociad2
#> Negative: Neurog3, Btbd17, Gadd45a, Ppp1r14a, Neurod2, Sox4, Smarcd2, Mdk, Pax4, Btg2
#> Sult2b1, Hes6, Grasp, Igfbpl1, Gpx2, Cbfa2t3, Foxa3, Shf, Mfng, Tmsb4x
#> Amotl2, Gdpd1, Cdc14b, Epb42, Rcor2, Cotl1, Upk3bl, Rbfox3, Cldn6, Cer1
#> StandardPC_ 3
#> Positive: Nusap1, Top2a, Birc5, Aurkb, Cdca8, Pbk, Mki67, Tpx2, Plk1, Ccnb1
#> 2810417H13Rik, Incenp, Cenpf, Ccna2, Prc1, Racgap1, Cdk1, Aurka, Cdca3, Hmmr
#> Spc24, Kif23, Sgol1, Cenpe, Cdc20, Hist1h1b, Cdca2, Mxd3, Kif22, Ska1
#> Negative: Anxa5, Pdzk1ip1, Acot1, Tpm1, Anxa2, Dcdc2a, Capg, Sparc, Ttr, Pamr1
#> Clu, Cxcl12, Ndrg2, Hnf1aos1, Gas6, Gsta3, Krt18, Ces1d, Atp1b1, Muc1
#> Hhex, Acadm, Spp1, Enpp2, Bcl2l14, Sat1, Smtnl2, 1700011H14Rik, Tgm2, Fam159a
#> StandardPC_ 4
#> Positive: Glud1, Tm4sf4, Akr1c19, Cldn4, Runx1t1, Fev, Pou3f4, Gm43861, Pgrmc1, Arx
#> Cd200, Lrpprc, Hmgn3, Ppp1r14c, Pam, Etv1, Tsc22d1, Slc25a5, Akap17b, Pgf
#> Fam43a, Emb, Jun, Krt8, Dnajc12, Mid1ip1, Ids, Rgs17, Uchl1, Alcam
#> Negative: Ins2, Ins1, Ppp1r1a, Nnat, Calr, Sytl4, Sdf2l1, Iapp, Pdia6, Mapt
#> G6pc2, C2cd4b, Npy, Gng12, P2ry1, Ero1lb, Adra2a, Papss2, Arhgap36, Fam151a
#> Dlk1, Creld2, Gip, Tmem215, Gm27033, Cntfr, Prss53, C2cd4a, Lyve1, Ociad2
#> StandardPC_ 5
#> Positive: Pdx1, Nkx6-1, Npepl1, Cldn4, Cryba2, Fev, Jun, Chgb, Gng12, Adra2a
#> Mnx1, Sytl4, Pdk3, Gm27033, Nnat, Chga, Ins2, 1110012L19Rik, Enho, Krt7
#> Mlxipl, Tmsb10, Flrt1, Pax4, Tubb3, Prrg2, Gars, Frzb, BC023829, Gm2694
#> Negative: Irx2, Irx1, Gcg, Ctxn2, Tmem27, Ctsz, Tmsb15l, Nap1l5, Pou6f2, Gria2
#> Ghrl, Peg10, Smarca1, Arx, Lrpap1, Rgs4, Ttr, Gast, Tmsb15b2, Serpina1b
#> Slc16a10, Wnk3, Ly6e, Auts2, Sct, Arg1, Dusp10, Sphkap, Dock11, Edn3
#> ℹ [2025-11-13 11:35:11] Perform `Seurat::FindClusters()` with louvain and `cluster_resolution` = 0.6
#> ℹ [2025-11-13 11:35:11] Reorder clusters...
#> First group.by variable `ident` starts with a number, appending `g` to ensure valid variable names
#> This message is displayed once every 8 hours.
#> ℹ [2025-11-13 11:35:11] Perform umap nonlinear dimension reduction
#> ℹ [2025-11-13 11:35:11] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-11-13 11:35:11] UMAP will return its model
#> ℹ [2025-11-13 11:35:13] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-11-13 11:35:13] UMAP will return its model
#> ✔ [2025-11-13 11:35:15] Run scop standard workflow done
pancreas_sub <- RunCellChat(
pancreas_sub,
group.by = "CellType",
species = "mouse"
)
#> ℹ [2025-11-13 11:35:15] Start CellChat analysis
#> ◌ [2025-11-13 11:35:15] Installing: CellChat...
#> ℹ Loading metadata database
#> ✔ Loading metadata database ... done
#>
#>
#> → Will install 151 packages.
#> → Will download 1 CRAN package (1.68 MB), cached: 150 (0 B).
#> + Biobase 2.70.0 [bld][cmp]
#> + BiocGenerics 0.56.0 [bld]
#> + BiocManager 1.30.26
#> + BiocNeighbors 2.4.0 [bld][cmp]
#> + CellChat 2.2.0 [bld][cmp] (GitHub: 623f48f)
#> + ComplexHeatmap 2.26.0 [bld]
#> + Deriv 4.2.0
#> + FNN 1.1.4.1
#> + Formula 1.2-5
#> + GetoptLong 1.0.5 + ✔ perl
#> + GlobalOptions 0.1.2
#> + IRanges 2.44.0 [bld][cmp]
#> + MatrixModels 0.5-4
#> + NMF 0.28 [bld][cmp][dl] (1.68 MB)
#> + R6 2.6.1
#> + RColorBrewer 1.1-3
#> + RSpectra 0.16-2
#> + Rcpp 1.1.0
#> + RcppEigen 0.3.4.0.2
#> + RcppTOML 0.2.3
#> + Rdpack 2.6.4
#> + S4Vectors 0.48.0 [bld][cmp]
#> + S7 0.2.0
#> + SparseM 1.84-2
#> + abind 1.4-8
#> + askpass 1.2.1
#> + assorthead 1.4.0 [bld]
#> + backports 1.5.0
#> + base64enc 0.1-3
#> + broom 1.0.10
#> + bslib 0.9.0
#> + cachem 1.1.0
#> + car 3.1-3
#> + carData 3.0-5
#> + circlize 0.4.16
#> + cli 3.6.5
#> + clue 0.3-66
#> + coda 0.19-4.1
#> + colorspace 2.1-2
#> + commonmark 2.0.0
#> + corrplot 0.95
#> + cowplot 1.2.0
#> + crayon 1.5.3
#> + crosstalk 1.2.2
#> + curl 7.0.0 + ✔ libcurl4-openssl-dev, ✔ libssl-dev
#> + data.table 1.17.8
#> + digest 0.6.37
#> + doBy 4.7.0
#> + doParallel 1.0.17
#> + dplyr 1.1.4
#> + evaluate 1.0.5
#> + farver 2.1.2
#> + fastmap 1.2.0
#> + fontawesome 0.5.3
#> + foreach 1.5.2
#> + fs 1.6.6 + ✔ make
#> + future 1.67.0
#> + future.apply 1.20.0
#> + generics 0.1.4
#> + ggalluvial 0.12.5
#> + ggnetwork 0.5.14
#> + ggplot2 4.0.0
#> + ggpubr 0.6.2
#> + ggrepel 0.9.6
#> + ggsci 4.1.0
#> + ggsignif 0.6.4
#> + globals 0.18.0
#> + glue 1.8.0
#> + gridBase 0.4-7
#> + gridExtra 2.3
#> + gtable 0.3.6
#> + here 1.0.2
#> + highr 0.11
#> + htmltools 0.5.8.1
#> + htmlwidgets 1.6.4
#> + httpuv 1.6.16 + ✔ make, ✔ zlib1g-dev
#> + httr 1.4.7
#> + igraph 2.2.1 + ✔ libglpk-dev, ✔ libxml2-dev
#> + irlba 2.3.5.1
#> + isoband 0.2.7
#> + iterators 1.0.14
#> + jquerylib 0.1.4
#> + jsonlite 2.0.0
#> + knitr 1.50 + ✔ pandoc
#> + labeling 0.4.3
#> + later 1.4.4
#> + lazyeval 0.2.2
#> + lifecycle 1.0.4
#> + listenv 0.10.0
#> + lme4 1.1-37
#> + magrittr 2.0.4
#> + matrixStats 1.5.0
#> + memoise 2.0.1
#> + microbenchmark 1.5.0
#> + mime 0.13
#> + minqa 1.2.8 + ✔ make
#> + modelr 0.1.11
#> + network 1.19.0
#> + nloptr 2.2.1 + ✔ cmake
#> + numDeriv 2016.8-1.1
#> + openssl 2.3.4 + ✔ libssl-dev
#> + otel 0.2.0
#> + parallelly 1.45.1
#> + patchwork 1.3.2
#> + pbapply 1.7-4
#> + pbkrtest 0.5.5
#> + pillar 1.11.1
#> + pkgconfig 2.0.3
#> + plotly 4.11.0
#> + plyr 1.8.9
#> + png 0.1-8 + ✔ libpng-dev
#> + polynom 1.4-1
#> + promises 1.5.0
#> + purrr 1.2.0
#> + quantreg 6.1
#> + rappdirs 0.3.3
#> + rbibutils 2.4
#> + reformulas 0.4.2
#> + registry 0.5-1
#> + reshape2 1.4.4
#> + reticulate 1.44.0 + ✔ python3
#> + rjson 0.2.23
#> + rlang 1.1.6
#> + rmarkdown 2.30 + ✔ pandoc
#> + rngtools 1.5.2
#> + rprojroot 2.1.1
#> + rstatix 0.7.3
#> + sass 0.4.10 + ✔ make
#> + scales 1.4.0
#> + shape 1.4.6.1
#> + shiny 1.11.1
#> + sna 2.8
#> + sourcetools 0.1.7-1
#> + statnet.common 4.12.0
#> + stringi 1.8.7 + ✔ libicu-dev
#> + stringr 1.6.0
#> + svglite 2.2.2 + ✔ libpng-dev
#> + sys 3.4.3
#> + systemfonts 1.3.1 + ✔ libfontconfig1-dev, ✔ libfreetype6-dev
#> + textshaping 1.0.4 + ✔ libfreetype6-dev, ✔ libfribidi-dev, ✔ libharfbuzz-dev
#> + tibble 3.3.0
#> + tidyr 1.3.1
#> + tidyselect 1.2.1
#> + tinytex 0.57
#> + utf8 1.2.6
#> + vctrs 0.6.5
#> + viridisLite 0.4.2
#> + withr 3.0.2
#> + xfun 0.54
#> + xtable 1.8-4
#> + yaml 2.3.10
#> ✔ All system requirements are already installed.
#>
#> ℹ Getting 1 pkg (1.68 MB), 150 cached
#> ✔ Cached copy of NMF 0.28 (source) is the latest build
#> ✔ Got CellChat 2.2.0 (source) (29.82 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libcurl4-openssl-dev libssl-dev make perl zlib1g-dev libglpk-dev libxml2-dev pandoc cmake libpng-dev python3 libicu-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.6).
#> make is already the newest version (4.3-4.1build2).
#> perl is already the newest version (5.38.2-3.2ubuntu0.2).
#> zlib1g-dev is already the newest version (1:1.3.dfsg-3.1ubuntu2.1).
#> libglpk-dev is already the newest version (5.0-1build2).
#> libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.6).
#> pandoc is already the newest version (3.1.3+ds-2).
#> cmake is already the newest version (3.28.3-1build7).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> python3 is already the newest version (3.12.3-0ubuntu2.1).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> libfontconfig1-dev is already the newest version (2.15.0-1.1ubuntu2).
#> libfreetype-dev is already the newest version (2.13.2+dfsg-1build3).
#> libfribidi-dev is already the newest version (1.0.13-3build1).
#> libharfbuzz-dev is already the newest version (8.3.0-2build2).
#> 0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
#> ℹ Building assorthead 1.4.0
#> ✔ Installed abind 1.4-8 (79ms)
#> ✔ Installed askpass 1.2.1 (132ms)
#> ✔ Installed backports 1.5.0 (180ms)
#> ✔ Installed base64enc 0.1-3 (72ms)
#> ✔ Installed BiocManager 1.30.26 (72ms)
#> ✔ Installed broom 1.0.10 (103ms)
#> ✔ Installed bslib 0.9.0 (1.1s)
#> ✔ Installed cachem 1.1.0 (1.1s)
#> ✔ Installed car 3.1-3 (76ms)
#> ✔ Installed carData 3.0-5 (76ms)
#> ✔ Installed circlize 0.4.16 (77ms)
#> ✔ Installed cli 3.6.5 (74ms)
#> ✔ Installed clue 0.3-66 (110ms)
#> ✔ Installed coda 0.19-4.1 (121ms)
#> ✔ Installed colorspace 2.1-2 (81ms)
#> ✔ Installed commonmark 2.0.0 (73ms)
#> ✔ Installed corrplot 0.95 (77ms)
#> ✔ Installed cowplot 1.2.0 (73ms)
#> ✔ Installed crayon 1.5.3 (71ms)
#> ✔ Installed crosstalk 1.2.2 (119ms)
#> ✔ Installed curl 7.0.0 (98ms)
#> ✔ Installed data.table 1.17.8 (89ms)
#> ✔ Installed Deriv 4.2.0 (77ms)
#> ✔ Installed digest 0.6.37 (75ms)
#> ✔ Installed doBy 4.7.0 (91ms)
#> ✔ Built assorthead 1.4.0 (2.7s)
#> ✔ Installed doParallel 1.0.17 (155ms)
#> ✔ Installed dplyr 1.1.4 (157ms)
#> ✔ Installed evaluate 1.0.5 (70ms)
#> ✔ Installed farver 2.1.2 (66ms)
#> ✔ Installed fastmap 1.2.0 (64ms)
#> ✔ Installed FNN 1.1.4.1 (64ms)
#> ✔ Installed fontawesome 0.5.3 (65ms)
#> ✔ Installed foreach 1.5.2 (122ms)
#> ✔ Installed Formula 1.2-5 (79ms)
#> ✔ Installed fs 1.6.6 (67ms)
#> ✔ Installed future 1.67.0 (72ms)
#> ✔ Installed future.apply 1.20.0 (69ms)
#> ✔ Installed generics 0.1.4 (66ms)
#> ℹ Building BiocGenerics 0.56.0
#> ✔ Installed GetoptLong 1.0.5 (122ms)
#> ✔ Installed ggalluvial 0.12.5 (38ms)
#> ✔ Installed ggnetwork 0.5.14 (1s)
#> ✔ Installed ggpubr 0.6.2 (1s)
#> ✔ Installed ggplot2 4.0.0 (1.1s)
#> ✔ Installed ggrepel 0.9.6 (82ms)
#> ✔ Installed ggsci 4.1.0 (76ms)
#> ✔ Installed ggsignif 0.6.4 (71ms)
#> ✔ Installed GlobalOptions 0.1.2 (82ms)
#> ✔ Installed globals 0.18.0 (99ms)
#> ✔ Installed glue 1.8.0 (108ms)
#> ✔ Installed gridBase 0.4-7 (68ms)
#> ✔ Installed gridExtra 2.3 (67ms)
#> ✔ Installed gtable 0.3.6 (70ms)
#> ✔ Built BiocGenerics 0.56.0 (3s)
#> ✔ Installed here 1.0.2 (93ms)
#> ✔ Installed highr 0.11 (88ms)
#> ✔ Installed htmltools 0.5.8.1 (64ms)
#> ✔ Installed htmlwidgets 1.6.4 (95ms)
#> ✔ Installed httpuv 1.6.16 (68ms)
#> ✔ Installed httr 1.4.7 (67ms)
#> ✔ Installed irlba 2.3.5.1 (1s)
#> ✔ Installed igraph 2.2.1 (1.1s)
#> ✔ Installed isoband 0.2.7 (69ms)
#> ✔ Installed iterators 1.0.14 (64ms)
#> ✔ Installed jquerylib 0.1.4 (96ms)
#> ✔ Installed jsonlite 2.0.0 (68ms)
#> ✔ Installed knitr 1.50 (77ms)
#> ✔ Installed labeling 0.4.3 (74ms)
#> ✔ Installed later 1.4.4 (65ms)
#> ✔ Installed lazyeval 0.2.2 (65ms)
#> ✔ Installed lifecycle 1.0.4 (65ms)
#> ✔ Installed listenv 0.10.0 (65ms)
#> ✔ Installed lme4 1.1-37 (97ms)
#> ✔ Installed magrittr 2.0.4 (69ms)
#> ✔ Installed MatrixModels 0.5-4 (66ms)
#> ✔ Installed matrixStats 1.5.0 (67ms)
#> ✔ Installed memoise 2.0.1 (66ms)
#> ✔ Installed microbenchmark 1.5.0 (65ms)
#> ✔ Installed mime 0.13 (65ms)
#> ✔ Installed minqa 1.2.8 (93ms)
#> ✔ Installed modelr 0.1.11 (65ms)
#> ✔ Installed network 1.19.0 (67ms)
#> ✔ Installed nloptr 2.2.1 (67ms)
#> ✔ Installed NMF 0.28 (68ms)
#> ✔ Installed numDeriv 2016.8-1.1 (64ms)
#> ✔ Installed openssl 2.3.4 (63ms)
#> ✔ Installed otel 0.2.0 (97ms)
#> ✔ Installed parallelly 1.45.1 (68ms)
#> ✔ Installed patchwork 1.3.2 (69ms)
#> ✔ Installed pbapply 1.7-4 (67ms)
#> ✔ Installed pbkrtest 0.5.5 (66ms)
#> ✔ Installed pillar 1.11.1 (67ms)
#> ✔ Installed pkgconfig 2.0.3 (66ms)
#> ✔ Installed plotly 4.11.0 (1.1s)
#> ✔ Installed plyr 1.8.9 (1.1s)
#> ✔ Installed png 0.1-8 (65ms)
#> ✔ Installed polynom 1.4-1 (63ms)
#> ✔ Installed promises 1.5.0 (66ms)
#> ✔ Installed purrr 1.2.0 (68ms)
#> ✔ Installed quantreg 6.1 (66ms)
#> ✔ Installed R6 2.6.1 (95ms)
#> ✔ Installed rappdirs 0.3.3 (96ms)
#> ✔ Installed rbibutils 2.4 (69ms)
#> ✔ Installed RColorBrewer 1.1-3 (63ms)
#> ✔ Installed Rcpp 1.1.0 (71ms)
#> ✔ Installed RcppEigen 0.3.4.0.2 (86ms)
#> ✔ Installed RcppTOML 0.2.3 (64ms)
#> ✔ Installed Rdpack 2.6.4 (63ms)
#> ✔ Installed reformulas 0.4.2 (120ms)
#> ✔ Installed registry 0.5-1 (60ms)
#> ✔ Installed reshape2 1.4.4 (60ms)
#> ✔ Installed reticulate 1.44.0 (66ms)
#> ✔ Installed rjson 0.2.23 (64ms)
#> ✔ Installed rlang 1.1.6 (63ms)
#> ✔ Installed rmarkdown 2.30 (72ms)
#> ✔ Installed rngtools 1.5.2 (104ms)
#> ✔ Installed rprojroot 2.1.1 (66ms)
#> ✔ Installed RSpectra 0.16-2 (66ms)
#> ✔ Installed rstatix 0.7.3 (69ms)
#> ✔ Installed S7 0.2.0 (69ms)
#> ✔ Installed sass 0.4.10 (80ms)
#> ✔ Installed scales 1.4.0 (67ms)
#> ✔ Installed shape 1.4.6.1 (97ms)
#> ✔ Installed shiny 1.11.1 (103ms)
#> ✔ Installed sna 2.8 (70ms)
#> ✔ Installed sourcetools 0.1.7-1 (63ms)
#> ✔ Installed SparseM 1.84-2 (65ms)
#> ✔ Installed statnet.common 4.12.0 (63ms)
#> ✔ Installed stringr 1.6.0 (1s)
#> ✔ Installed stringi 1.8.7 (1.1s)
#> ✔ Installed svglite 2.2.2 (100ms)
#> ✔ Installed sys 3.4.3 (67ms)
#> ✔ Installed systemfonts 1.3.1 (67ms)
#> ✔ Installed textshaping 1.0.4 (71ms)
#> ✔ Installed tibble 3.3.0 (68ms)
#> ✔ Installed tidyr 1.3.1 (66ms)
#> ✔ Installed tidyselect 1.2.1 (65ms)
#> ✔ Installed tinytex 0.57 (99ms)
#> ✔ Installed utf8 1.2.6 (65ms)
#> ✔ Installed vctrs 0.6.5 (65ms)
#> ✔ Installed viridisLite 0.4.2 (66ms)
#> ✔ Installed withr 3.0.2 (65ms)
#> ✔ Installed xfun 0.54 (64ms)
#> ✔ Installed xtable 1.8-4 (64ms)
#> ✔ Installed yaml 2.3.10 (96ms)
#> ✔ Installed BiocGenerics 0.56.0 (1s)
#> ℹ Building Biobase 2.70.0
#> ✔ Installed assorthead 1.4.0 (1.1s)
#> ℹ Building BiocNeighbors 2.4.0
#> ℹ Building S4Vectors 0.48.0
#> ✔ Built Biobase 2.70.0 (9.8s)
#> ✔ Installed Biobase 2.70.0 (49ms)
#> ✔ Built S4Vectors 0.48.0 (18.4s)
#> ✔ Installed S4Vectors 0.48.0 (50ms)
#> ℹ Building IRanges 2.44.0
#> ✔ Built BiocNeighbors 2.4.0 (32.2s)
#> ✔ Installed BiocNeighbors 2.4.0 (80ms)
#> ✔ Built IRanges 2.44.0 (37s)
#> ✔ Installed IRanges 2.44.0 (1s)
#> ℹ Building ComplexHeatmap 2.26.0
#> ✔ Built ComplexHeatmap 2.26.0 (12.7s)
#> ✔ Installed ComplexHeatmap 2.26.0 (37ms)
#> ℹ Packaging CellChat 2.2.0
#> ✔ Packaged CellChat 2.2.0 (4.2s)
#> ℹ Building CellChat 2.2.0
#> ✔ Built CellChat 2.2.0 (24.6s)
#> ✔ Installed CellChat 2.2.0 (github::jinworks/CellChat@623f48f) (62ms)
#> ✔ 1 pkg + 160 deps: kept 9, added 151, dld 1 (NA B) [2m 15.8s]
#> ✔ [2025-11-13 11:37:31] jinworks/CellChat installed successfully
#> ◌ [2025-11-13 11:37:31] Installing: presto...
#>
#> → Will install 2 packages.
#> → All 2 packages (0 B) are cached.
#> + RcppArmadillo 15.0.2-2
#> + presto 1.0.0 [bld][cmp] (GitHub: 7636b3d)
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 2 pkgs are cached
#> ✔ Got presto 1.0.0 (source) (746.05 kB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
#> ✔ Installed RcppArmadillo 15.0.2-2 (91ms)
#> ℹ Packaging presto 1.0.0
#> ✔ Packaged presto 1.0.0 (715ms)
#> ℹ Building presto 1.0.0
#> ✔ Built presto 1.0.0 (12.3s)
#> ✔ Installed presto 1.0.0 (github::immunogenomics/presto@7636b3d) (34ms)
#> ✔ 1 pkg + 24 deps: kept 23, added 2, dld 1 (NA B) [17.7s]
#> ✔ [2025-11-13 11:37:49] immunogenomics/presto installed successfully
#> [1] "Create a CellChat object from a data matrix"
#> Set cell identities for the new CellChat object
#> The cell groups used for CellChat analysis are Ductal, Ngn3-high-EP, Endocrine, Ngn3-low-EP, Pre-endocrine
#> The number of highly variable ligand-receptor pairs used for signaling inference is 841
#> triMean is used for calculating the average gene expression per cell group.
#> [1] ">>> Run CellChat on sc/snRNA-seq data <<< [2025-11-13 11:37:51.449952]"
#> [1] ">>> CellChat inference is done. Parameter values are stored in `object@options$parameter` <<< [2025-11-13 11:39:02.205628]"
#> ✔ [2025-11-13 11:39:02] CellChat analysis completed
CellChatPlot(pancreas_sub, plot_type = "aggregate")
#> ℹ [2025-11-13 11:39:02] Creating "aggregate" plot for condition "ALL"
#> Signaling role analysis on the aggregated cell-cell communication network from all signaling pathways
#> ✔ [2025-11-13 11:39:02] Plot creation completed
CellChatPlot(pancreas_sub, plot_type = "pathway")
#> ℹ [2025-11-13 11:39:03] Creating "pathway" plot for condition "ALL"
#> ℹ [2025-11-13 11:39:03] Using top 10 pathways
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> ✔ [2025-11-13 11:39:07] Plot creation completed
#> NULL
CellChatPlot(pancreas_sub, plot_type = "bubble")
#> ℹ [2025-11-13 11:39:07] Creating "bubble" plot for condition "ALL"
#> ℹ [2025-11-13 11:39:07] No pathway specified. Using top 3 pathways for bubble plots
#> Comparing communications on a single object
#> Comparing communications on a single object
#> Comparing communications on a single object
#> ✔ [2025-11-13 11:39:07] Plot creation completed
CellChatPlot(pancreas_sub, plot_type = "gene")
#> ℹ [2025-11-13 11:39:08] Creating "gene" plot for condition "ALL"
#> ℹ [2025-11-13 11:39:08] No pathway specified. Using top 3 pathways for gene expression plots
#> ✔ [2025-11-13 11:39:08] Plot creation completed
CellChatPlot(pancreas_sub, plot_type = "heatmap")
#> ℹ [2025-11-13 11:39:10] Creating "heatmap" plot for condition "ALL"
#> ✔ [2025-11-13 11:39:12] Plot creation completed
#> NULL