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 is"png".- top_n
Number of top pathways to use for plotting. Default is
10.- base_height
Base height multiplier for all plots. Default is
1.- base_width
Base width multiplier for all plots. Default is
1.- res
Resolution for PNG output. Default is
300.- verbose
Whether to print the message. Default is
TRUE.
Examples
options(log_message.verbose = FALSE)
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> 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
#> First group.by variable `ident` starts with a number, appending `g` to ensure valid variable names
#> This message is displayed once every 8 hours.
pancreas_sub <- RunCellChat(
pancreas_sub,
group.by = "CellType",
species = "mouse"
)
#> ℹ Loading metadata database
#> ✔ Loading metadata database ... done
#>
#>
#> → Will install 170 packages.
#> → All 170 packages (0 B) are cached.
#> + BH 1.87.0-1
#> + Biobase 2.70.0 [bld][cmp]
#> + BiocGenerics 0.56.0 [bld]
#> + BiocManager 1.30.27
#> + BiocParallel 1.44.0 [bld][cmp]
#> + BiocStyle 2.38.0 [bld]
#> + DESeq2 1.50.2 [bld][cmp]
#> + DelayedArray 0.36.0 [bld][cmp]
#> + FNN 1.1.4.1
#> + GenomicRanges 1.62.0 [bld][cmp]
#> + IRanges 2.44.0 [bld][cmp]
#> + MatrixGenerics 1.22.0 [bld]
#> + R6 2.6.1
#> + RANN 2.6.2
#> + RColorBrewer 1.1-3
#> + ROCR 1.0-11
#> + RSpectra 0.16-2
#> + Rcpp 1.1.0
#> + RcppAnnoy 0.0.22
#> + RcppArmadillo 15.2.2-1
#> + RcppHNSW 0.6.0
#> + RcppTOML 0.2.3
#> + Rtsne 0.17
#> + S4Arrays 1.10.1 [bld][cmp]
#> + S4Vectors 0.48.0 [bld][cmp]
#> + S7 0.2.1
#> + Seqinfo 1.0.0 [bld]
#> + Seurat 5.3.1
#> + SeuratObject 5.2.0
#> + SingleCellExperiment 1.32.0 [bld]
#> + SparseArray 1.10.4 [bld][cmp]
#> + SummarizedExperiment 1.40.0 [bld]
#> + XVector 0.50.0 [bld][cmp]
#> + abind 1.4-8
#> + askpass 1.2.1
#> + backports 1.5.0
#> + base64enc 0.1-3
#> + bitops 1.0-9
#> + bookdown 0.45 + ✔ pandoc
#> + brio 1.1.5
#> + broom 1.0.11
#> + bslib 0.9.0
#> + caTools 1.18.3
#> + cachem 1.1.0
#> + callr 3.7.6
#> + cli 3.6.5
#> + commonmark 2.0.0
#> + cowplot 1.2.0
#> + cpp11 0.5.2
#> + crayon 1.5.3
#> + crosstalk 1.2.2
#> + curl 7.0.0 + ✔ libcurl4-openssl-dev, ✔ libssl-dev
#> + data.table 1.17.8
#> + deldir 2.0-4
#> + desc 1.4.3
#> + diffobj 0.3.6
#> + digest 0.6.39
#> + dotCall64 1.2
#> + dplyr 1.1.4
#> + evaluate 1.0.5
#> + farver 2.1.2
#> + fastDummies 1.7.5
#> + fastmap 1.2.0
#> + fitdistrplus 1.2-4
#> + fontawesome 0.5.3
#> + formatR 1.14
#> + fs 1.6.6 + ✔ make
#> + futile.logger 1.4.3
#> + futile.options 1.0.1
#> + future 1.68.0
#> + future.apply 1.20.0
#> + generics 0.1.4
#> + ggplot2 4.0.1
#> + ggrepel 0.9.6
#> + ggridges 0.5.7
#> + globals 0.18.0
#> + glue 1.8.0
#> + goftest 1.2-3
#> + gplots 3.3.0
#> + gridExtra 2.3
#> + gtable 0.3.6
#> + gtools 3.9.5
#> + here 1.0.2
#> + highr 0.11
#> + htmltools 0.5.9
#> + htmlwidgets 1.6.4
#> + httpuv 1.6.16 + ✔ make, ✔ zlib1g-dev
#> + httr 1.4.7
#> + ica 1.0-3
#> + igraph 2.2.1 + ✔ libglpk-dev, ✔ libxml2-dev
#> + irlba 2.3.5.1
#> + isoband 0.2.7
#> + jquerylib 0.1.4
#> + jsonlite 2.0.0
#> + knitr 1.50 + ✔ pandoc
#> + labeling 0.4.3
#> + lambda.r 1.2.4
#> + later 1.4.4
#> + lazyeval 0.2.2
#> + leidenbase 0.1.35
#> + lifecycle 1.0.4
#> + listenv 0.10.0
#> + lmtest 0.9-40
#> + locfit 1.5-9.12
#> + magrittr 2.0.4
#> + matrixStats 1.5.0
#> + memoise 2.0.1
#> + mime 0.13
#> + miniUI 0.1.2
#> + openssl 2.3.4 + ✔ libssl-dev
#> + otel 0.2.0
#> + parallelly 1.45.1
#> + patchwork 1.3.2
#> + pbapply 1.7-4
#> + pillar 1.11.1
#> + pkgbuild 1.4.8
#> + pkgconfig 2.0.3
#> + pkgload 1.4.1
#> + plotly 4.11.0
#> + plyr 1.8.9
#> + png 0.1-8 + ✔ libpng-dev
#> + polyclip 1.10-7
#> + praise 1.0.0
#> + presto 1.0.0 [bld][cmp] (GitHub: 7636b3d)
#> + processx 3.8.6
#> + progressr 0.18.0
#> + promises 1.5.0
#> + ps 1.9.1
#> + purrr 1.2.0
#> + rappdirs 0.3.3
#> + reshape2 1.4.5
#> + reticulate 1.44.1 + ✔ python3
#> + rlang 1.1.6
#> + rmarkdown 2.30 + ✔ pandoc
#> + rprojroot 2.1.1
#> + sass 0.4.10 + ✔ make
#> + scales 1.4.0
#> + scattermore 1.2
#> + sctransform 0.4.2
#> + shiny 1.12.0
#> + snow 0.4-4
#> + sourcetools 0.1.7-1
#> + sp 2.2-0
#> + spam 2.11-1
#> + spatstat.data 3.1-9
#> + spatstat.explore 3.6-0
#> + spatstat.geom 3.6-1
#> + spatstat.random 3.4-3
#> + spatstat.sparse 3.1-0
#> + spatstat.univar 3.1-5
#> + spatstat.utils 3.2-0
#> + stringi 1.8.7 + ✔ libicu-dev
#> + stringr 1.6.0
#> + sys 3.4.3
#> + tensor 1.5.1
#> + testthat 3.3.1
#> + tibble 3.3.0
#> + tidyr 1.3.1
#> + tidyselect 1.2.1
#> + tinytex 0.58
#> + utf8 1.2.6
#> + uwot 0.2.4
#> + vctrs 0.6.5
#> + viridisLite 0.4.2
#> + waldo 0.6.2
#> + withr 3.0.2
#> + xfun 0.54
#> + xtable 1.8-4
#> + yaml 2.3.11
#> + zoo 1.8-14
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 170 pkgs are cached
#> ✔ Got askpass 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (21.89 kB)
#> ✔ Got base64enc 0.1-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (26.57 kB)
#> ✔ Got abind 1.4-8 (x86_64-pc-linux-gnu-ubuntu-24.04) (64.92 kB)
#> ✔ Got backports 1.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (115.90 kB)
#> ✔ Got BiocGenerics 0.56.0 (source) (61.53 kB)
#> ✔ Got lifecycle 1.0.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (125.07 kB)
#> ✔ Got gtable 0.3.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (222.55 kB)
#> ✔ Got rprojroot 2.1.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (113.23 kB)
#> ✔ Got gtools 3.9.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (361.11 kB)
#> ✔ Got rappdirs 0.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (45.26 kB)
#> ✔ Got DelayedArray 0.36.0 (source) (816.30 kB)
#> ✔ Got BiocStyle 2.38.0 (source) (908.65 kB)
#> ✔ Got BiocManager 1.30.27 (x86_64-pc-linux-gnu-ubuntu-24.04) (666.57 kB)
#> ✔ Got xtable 1.8-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (706.31 kB)
#> ✔ Got MatrixGenerics 1.22.0 (source) (34.60 kB)
#> ✔ Got RSpectra 0.16-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (529.66 kB)
#> ✔ Got BiocParallel 1.44.0 (source) (1.11 MB)
#> ✔ Got XVector 0.50.0 (source) (71.42 kB)
#> ✔ Got tensor 1.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (13.96 kB)
#> ✔ Got gridExtra 2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.11 MB)
#> ✔ Got spatstat.sparse 3.1-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (213.31 kB)
#> ✔ Got IRanges 2.44.0 (source) (496.06 kB)
#> ✔ Got cpp11 0.5.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (289.40 kB)
#> ✔ Got desc 1.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (334.52 kB)
#> ✔ Got GenomicRanges 1.62.0 (source) (1.38 MB)
#> ✔ Got Biobase 2.70.0 (source) (1.98 MB)
#> ✔ Got curl 7.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (788.30 kB)
#> ✔ Got zoo 1.8-14 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.03 MB)
#> ✔ Got fastmap 1.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (66.05 kB)
#> ✔ Got DESeq2 1.50.2 (source) (2.69 MB)
#> ✔ Got RcppArmadillo 15.2.2-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.70 MB)
#> ✔ Got FNN 1.1.4.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (128.22 kB)
#> ✔ Got dplyr 1.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.49 MB)
#> ✔ Got fs 1.6.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (310.07 kB)
#> ✔ Got goftest 1.2-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (58.64 kB)
#> ✔ Got farver 2.1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.47 MB)
#> ✔ Got here 1.0.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (53.59 kB)
#> ✔ Got magrittr 2.0.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (221.44 kB)
#> ✔ Got httr 1.4.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (486.52 kB)
#> ✔ Got listenv 0.10.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (106.64 kB)
#> ✔ Got htmlwidgets 1.6.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (815.05 kB)
#> ✔ Got pkgload 1.4.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (222.06 kB)
#> ✔ Got knitr 1.50 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.10 MB)
#> ✔ Got polyclip 1.10-7 (x86_64-pc-linux-gnu-ubuntu-24.04) (120.02 kB)
#> ✔ Got ps 1.9.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (499.64 kB)
#> ✔ Got R6 2.6.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (86.81 kB)
#> ✔ Got locfit 1.5-9.12 (x86_64-pc-linux-gnu-ubuntu-24.04) (539.82 kB)
#> ✔ Got processx 3.8.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (337.39 kB)
#> ✔ Got ROCR 1.0-11 (x86_64-pc-linux-gnu-ubuntu-24.04) (465.58 kB)
#> ✔ Got reshape2 1.4.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (122.33 kB)
#> ✔ Got rlang 1.1.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.59 MB)
#> ✔ Got presto 1.0.0 (source) (746.05 kB)
#> ✔ Got Rcpp 1.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.19 MB)
#> ✔ Got plotly 4.11.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.86 MB)
#> ✔ Got rmarkdown 2.30 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.64 MB)
#> ✔ Got spatstat.utils 3.2-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (401.56 kB)
#> ✔ Got SeuratObject 5.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.08 MB)
#> ✔ Got stringr 1.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (333.76 kB)
#> ✔ Got ggplot2 4.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (8.47 MB)
#> ✔ Got waldo 0.6.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (135.16 kB)
#> ✔ Got Seurat 5.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.70 MB)
#> ✔ Got tinytex 0.58 (x86_64-pc-linux-gnu-ubuntu-24.04) (143.77 kB)
#> ✔ Got yaml 2.3.11 (x86_64-pc-linux-gnu-ubuntu-24.04) (115.50 kB)
#> ✔ Got vctrs 0.6.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.31 MB)
#> ✔ Got spam 2.11-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.75 MB)
#> ✔ Got Seqinfo 1.0.0 (source) (254.66 kB)
#> ✔ Got S4Vectors 0.48.0 (source) (843.90 kB)
#> ✔ Got SummarizedExperiment 1.40.0 (source) (690.87 kB)
#> ✔ Got testthat 3.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.11 MB)
#> ✔ Got tidyr 1.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.18 MB)
#> ✔ Got caTools 1.18.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (205.11 kB)
#> ✔ Got fastDummies 1.7.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (41.76 kB)
#> ✔ Got SingleCellExperiment 1.32.0 (source) (987.98 kB)
#> ✔ Got dotCall64 1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (31.26 kB)
#> ✔ Got bookdown 0.45 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.09 MB)
#> ✔ Got cli 3.6.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.34 MB)
#> ✔ Got diffobj 0.3.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.00 MB)
#> ✔ Got globals 0.18.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (158.33 kB)
#> ✔ Got BH 1.87.0-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (13.35 MB)
#> ✔ Got futile.logger 1.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (96.77 kB)
#> ✔ Got ggrepel 0.9.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (290.23 kB)
#> ✔ Got glue 1.8.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (168.12 kB)
#> ✔ Got cowplot 1.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.38 MB)
#> ✔ Got future 1.68.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (966.66 kB)
#> ✔ Got httpuv 1.6.16 (x86_64-pc-linux-gnu-ubuntu-24.04) (656.07 kB)
#> ✔ Got highr 0.11 (x86_64-pc-linux-gnu-ubuntu-24.04) (37.50 kB)
#> ✔ Got labeling 0.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (60.95 kB)
#> ✔ Got data.table 1.17.8 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.67 MB)
#> ✔ Got pbapply 1.7-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (100.53 kB)
#> ✔ Got lambda.r 1.2.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (110.01 kB)
#> ✔ Got fontawesome 0.5.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.40 MB)
#> ✔ Got pkgbuild 1.4.8 (x86_64-pc-linux-gnu-ubuntu-24.04) (208.62 kB)
#> ✔ Got irlba 2.3.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (292.19 kB)
#> ✔ Got matrixStats 1.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (474.75 kB)
#> ✔ Got isoband 0.2.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.64 MB)
#> ✔ Got png 0.1-8 (x86_64-pc-linux-gnu-ubuntu-24.04) (40.57 kB)
#> ✔ Got praise 1.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (16.39 kB)
#> ✔ Got parallelly 1.45.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (571.86 kB)
#> ✔ Got RANN 2.6.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (43.84 kB)
#> ✔ Got RcppHNSW 0.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (217.19 kB)
#> ✔ Got openssl 2.3.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.31 MB)
#> ✔ Got sourcetools 0.1.7-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (46.59 kB)
#> ✔ Got progressr 0.18.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (412.00 kB)
#> ✔ Got scales 1.4.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (841.36 kB)
#> ✔ Got reticulate 1.44.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.98 MB)
#> ✔ Got spatstat.univar 3.1-5 (x86_64-pc-linux-gnu-ubuntu-24.04) (325.81 kB)
#> ✔ Got leidenbase 0.1.35 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.33 MB)
#> ✔ Got patchwork 1.3.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.35 MB)
#> ✔ Got spatstat.random 3.4-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.23 MB)
#> ✔ Got tibble 3.3.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (680.35 kB)
#> ✔ Got withr 3.0.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (223.90 kB)
#> ✔ Got utf8 1.2.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (151.81 kB)
#> ✔ Got brio 1.1.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (35.30 kB)
#> ✔ Got callr 3.7.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (449.24 kB)
#> ✔ Got crosstalk 1.2.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (412.02 kB)
#> ✔ Got digest 0.6.39 (x86_64-pc-linux-gnu-ubuntu-24.04) (230.38 kB)
#> ✔ Got spatstat.explore 3.6-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.56 MB)
#> ✔ Got uwot 0.2.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.03 MB)
#> ✔ Got deldir 2.0-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (278.91 kB)
#> ✔ Got stringi 1.8.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.29 MB)
#> ✔ Got formatR 1.14 (x86_64-pc-linux-gnu-ubuntu-24.04) (151.65 kB)
#> ✔ Got future.apply 1.20.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (191.24 kB)
#> ✔ Got memoise 2.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (48.86 kB)
#> ✔ Got miniUI 0.1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (35.20 kB)
#> ✔ Got ica 1.0-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (85.54 kB)
#> ✔ Got otel 0.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (279.62 kB)
#> ✔ Got pillar 1.11.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (660.46 kB)
#> ✔ Got lmtest 0.9-40 (x86_64-pc-linux-gnu-ubuntu-24.04) (403.49 kB)
#> ✔ Got RColorBrewer 1.1-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (51.81 kB)
#> ✔ Got RcppAnnoy 0.0.22 (x86_64-pc-linux-gnu-ubuntu-24.04) (269.84 kB)
#> ✔ Got sp 2.2-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.31 MB)
#> ✔ Got ggridges 0.5.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.25 MB)
#> ✔ Got promises 1.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.67 MB)
#> ✔ Got S7 0.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (325.15 kB)
#> ✔ Got bslib 0.9.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.67 MB)
#> ✔ Got tidyselect 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (225.28 kB)
#> ✔ Got xfun 0.54 (x86_64-pc-linux-gnu-ubuntu-24.04) (583.00 kB)
#> ✔ Got cachem 1.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (67.49 kB)
#> ✔ Got commonmark 2.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (148.07 kB)
#> ✔ Got evaluate 1.0.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (102.86 kB)
#> ✔ Got sctransform 0.4.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (565.83 kB)
#> ✔ Got futile.options 1.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (18.42 kB)
#> ✔ Got lazyeval 0.2.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (157.44 kB)
#> ✔ Got sass 0.4.10 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.46 MB)
#> ✔ Got jsonlite 2.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.09 MB)
#> ✔ Got plyr 1.8.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (787.35 kB)
#> ✔ Got Rtsne 0.17 (x86_64-pc-linux-gnu-ubuntu-24.04) (118.33 kB)
#> ✔ Got sys 3.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (40.73 kB)
#> ✔ Got RcppTOML 0.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (244.01 kB)
#> ✔ Got bitops 1.0-9 (x86_64-pc-linux-gnu-ubuntu-24.04) (26.02 kB)
#> ✔ Got purrr 1.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (553.55 kB)
#> ✔ Got crayon 1.5.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (163.30 kB)
#> ✔ Got pkgconfig 2.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (18.08 kB)
#> ✔ Got later 1.4.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (155.03 kB)
#> ✔ Got igraph 2.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.84 MB)
#> ✔ Got generics 0.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (80.38 kB)
#> ✔ Got mime 0.13 (x86_64-pc-linux-gnu-ubuntu-24.04) (44.52 kB)
#> ✔ Got snow 0.4-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (97.07 kB)
#> ✔ Got jquerylib 0.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (526.85 kB)
#> ✔ Got viridisLite 0.4.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.30 MB)
#> ✔ Got scattermore 1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (339.10 kB)
#> ✔ Got spatstat.data 3.1-9 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.17 MB)
#> ✔ Got gplots 3.3.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.90 MB)
#> ✔ Got fitdistrplus 1.2-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.96 MB)
#> ✔ Got spatstat.geom 3.6-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.18 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:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> 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
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install pandoc libcurl4-openssl-dev libssl-dev make zlib1g-dev libglpk-dev libxml2-dev libpng-dev python3 libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> pandoc is already the newest version (3.1.3+ds-2).
#> 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).
#> 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).
#> 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).
#> 0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
#> ✔ Installed abind 1.4-8 (79ms)
#> ✔ Installed askpass 1.2.1 (93ms)
#> ✔ Installed backports 1.5.0 (112ms)
#> ✔ Installed base64enc 0.1-3 (141ms)
#> ✔ Installed BiocManager 1.30.27 (1s)
#> ✔ Installed BH 1.87.0-1 (1.1s)
#> ✔ Installed bitops 1.0-9 (64ms)
#> ✔ Installed bookdown 0.45 (71ms)
#> ✔ Installed brio 1.1.5 (71ms)
#> ✔ Installed broom 1.0.11 (135ms)
#> ✔ Installed bslib 0.9.0 (1.1s)
#> ✔ Installed cachem 1.1.0 (1.1s)
#> ✔ Installed callr 3.7.6 (65ms)
#> ✔ Installed caTools 1.18.3 (113ms)
#> ✔ Installed cli 3.6.5 (66ms)
#> ✔ Installed commonmark 2.0.0 (68ms)
#> ✔ Installed cowplot 1.2.0 (69ms)
#> ✔ Installed cpp11 0.5.2 (70ms)
#> ✔ Installed crayon 1.5.3 (67ms)
#> ✔ Installed crosstalk 1.2.2 (119ms)
#> ✔ Installed curl 7.0.0 (77ms)
#> ✔ Installed data.table 1.17.8 (81ms)
#> ✔ Installed deldir 2.0-4 (77ms)
#> ✔ Installed desc 1.4.3 (65ms)
#> ✔ Installed diffobj 0.3.6 (68ms)
#> ✔ Installed digest 0.6.39 (110ms)
#> ✔ Installed dotCall64 1.2 (117ms)
#> ✔ Installed dplyr 1.1.4 (69ms)
#> ✔ Installed evaluate 1.0.5 (69ms)
#> ✔ Installed farver 2.1.2 (67ms)
#> ✔ Installed fastDummies 1.7.5 (69ms)
#> ✔ Installed fastmap 1.2.0 (66ms)
#> ✔ Installed fitdistrplus 1.2-4 (116ms)
#> ✔ Installed FNN 1.1.4.1 (68ms)
#> ✔ Installed fontawesome 0.5.3 (66ms)
#> ✔ Installed formatR 1.14 (66ms)
#> ✔ Installed fs 1.6.6 (67ms)
#> ✔ Installed futile.logger 1.4.3 (69ms)
#> ✔ Installed futile.options 1.0.1 (118ms)
#> ✔ Installed future 1.68.0 (79ms)
#> ✔ Installed future.apply 1.20.0 (70ms)
#> ✔ Installed generics 0.1.4 (67ms)
#> ℹ Building BiocGenerics 0.56.0
#> ✔ Installed ggplot2 4.0.1 (435ms)
#> ✔ Installed ggrepel 0.9.6 (1.1s)
#> ✔ Installed globals 0.18.0 (1s)
#> ✔ Installed ggridges 0.5.7 (1.1s)
#> ✔ Installed glue 1.8.0 (107ms)
#> ✔ Installed goftest 1.2-3 (137ms)
#> ✔ Installed gridExtra 2.3 (1s)
#> ✔ Built BiocGenerics 0.56.0 (3.6s)
#> ✔ Installed gplots 3.3.0 (1.2s)
#> ✔ Installed gtable 0.3.6 (94ms)
#> ✔ Installed gtools 3.9.5 (125ms)
#> ✔ Installed here 1.0.2 (82ms)
#> ✔ Installed highr 0.11 (68ms)
#> ✔ Installed htmltools 0.5.9 (69ms)
#> ✔ Installed htmlwidgets 1.6.4 (71ms)
#> ✔ Installed httpuv 1.6.16 (74ms)
#> ✔ Installed httr 1.4.7 (121ms)
#> ✔ Installed ica 1.0-3 (87ms)
#> ✔ Installed irlba 2.3.5.1 (1s)
#> ✔ Installed igraph 2.2.1 (1.1s)
#> ✔ Installed isoband 0.2.7 (121ms)
#> ✔ Installed jquerylib 0.1.4 (68ms)
#> ✔ Installed jsonlite 2.0.0 (66ms)
#> ✔ Installed knitr 1.50 (78ms)
#> ✔ Installed labeling 0.4.3 (78ms)
#> ✔ Installed lambda.r 1.2.4 (64ms)
#> ✔ Installed later 1.4.4 (120ms)
#> ✔ Installed lazyeval 0.2.2 (71ms)
#> ✔ Installed leidenbase 0.1.35 (66ms)
#> ✔ Installed lifecycle 1.0.4 (68ms)
#> ✔ Installed listenv 0.10.0 (67ms)
#> ✔ Installed lmtest 0.9-40 (66ms)
#> ✔ Installed locfit 1.5-9.12 (120ms)
#> ✔ Installed magrittr 2.0.4 (74ms)
#> ✔ Installed matrixStats 1.5.0 (68ms)
#> ℹ Building MatrixGenerics 1.22.0
#> ✔ Installed memoise 2.0.1 (79ms)
#> ✔ Installed mime 0.13 (26ms)
#> ✔ Installed miniUI 0.1.2 (18ms)
#> ✔ Installed openssl 2.3.4 (77ms)
#> ✔ Installed otel 0.2.0 (106ms)
#> ✔ Installed parallelly 1.45.1 (146ms)
#> ✔ Installed patchwork 1.3.2 (89ms)
#> ✔ Installed pbapply 1.7-4 (80ms)
#> ✔ Installed pillar 1.11.1 (76ms)
#> ✔ Installed pkgbuild 1.4.8 (127ms)
#> ✔ Installed pkgconfig 2.0.3 (73ms)
#> ✔ Installed pkgload 1.4.1 (74ms)
#> ✔ Installed plotly 4.11.0 (1.1s)
#> ✔ Installed plyr 1.8.9 (1.1s)
#> ✔ Installed png 0.1-8 (104ms)
#> ✔ Installed polyclip 1.10-7 (78ms)
#> ✔ Installed praise 1.0.0 (72ms)
#> ✔ Installed processx 3.8.6 (80ms)
#> ✔ Installed progressr 0.18.0 (148ms)
#> ✔ Installed promises 1.5.0 (153ms)
#> ✔ Installed ps 1.9.1 (76ms)
#> ✔ Installed purrr 1.2.0 (75ms)
#> ✔ Built MatrixGenerics 1.22.0 (2.6s)
#> ✔ Installed R6 2.6.1 (95ms)
#> ✔ Installed RANN 2.6.2 (87ms)
#> ✔ Installed rappdirs 0.3.3 (123ms)
#> ✔ Installed RColorBrewer 1.1-3 (79ms)
#> ✔ Installed Rcpp 1.1.0 (69ms)
#> ✔ Installed RcppAnnoy 0.0.22 (75ms)
#> ✔ Installed RcppHNSW 0.6.0 (1.2s)
#> ✔ Installed RcppArmadillo 15.2.2-1 (1.3s)
#> ✔ Installed RcppTOML 0.2.3 (67ms)
#> ✔ Installed reshape2 1.4.5 (65ms)
#> ✔ Installed reticulate 1.44.1 (66ms)
#> ✔ Installed rlang 1.1.6 (68ms)
#> ✔ Installed rmarkdown 2.30 (79ms)
#> ✔ Installed ROCR 1.0-11 (104ms)
#> ✔ Installed rprojroot 2.1.1 (66ms)
#> ✔ Installed RSpectra 0.16-2 (66ms)
#> ✔ Installed Rtsne 0.17 (66ms)
#> ✔ Installed S7 0.2.1 (67ms)
#> ✔ Installed sass 0.4.10 (69ms)
#> ✔ Installed scales 1.4.0 (67ms)
#> ✔ Installed scattermore 1.2 (96ms)
#> ✔ Installed sctransform 0.4.2 (95ms)
#> ✔ Installed Seurat 5.3.1 (72ms)
#> ✔ Installed SeuratObject 5.2.0 (74ms)
#> ✔ Installed snow 0.4-4 (1s)
#> ℹ Building BiocParallel 1.44.0
#> ✔ Installed shiny 1.12.0 (1.1s)
#> ✔ Installed sourcetools 0.1.7-1 (27ms)
#> ✔ Installed sp 2.2-0 (1.1s)
#> ✔ Installed spam 2.11-1 (1s)
#> ✔ Installed spatstat.data 3.1-9 (1.1s)
#> ✔ Installed spatstat.explore 3.6-0 (95ms)
#> ✔ Installed spatstat.geom 3.6-1 (81ms)
#> ✔ Installed spatstat.random 3.4-3 (72ms)
#> ✔ Installed spatstat.sparse 3.1-0 (69ms)
#> ✔ Installed spatstat.univar 3.1-5 (108ms)
#> ✔ Installed spatstat.utils 3.2-0 (105ms)
#> ✔ Installed stringi 1.8.7 (78ms)
#> ✔ Installed stringr 1.6.0 (80ms)
#> ✔ Installed sys 3.4.3 (75ms)
#> ✔ Installed tensor 1.5.1 (67ms)
#> ✔ Installed testthat 3.3.1 (75ms)
#> ✔ Installed tibble 3.3.0 (79ms)
#> ✔ Installed tidyr 1.3.1 (106ms)
#> ✔ Installed tidyselect 1.2.1 (72ms)
#> ✔ Installed tinytex 0.58 (69ms)
#> ✔ Installed utf8 1.2.6 (70ms)
#> ✔ Installed uwot 0.2.4 (80ms)
#> ✔ Installed vctrs 0.6.5 (78ms)
#> ✔ Installed viridisLite 0.4.2 (72ms)
#> ✔ Installed waldo 0.6.2 (123ms)
#> ✔ Installed withr 3.0.2 (74ms)
#> ℹ Packaging presto 1.0.0
#> ✔ Installed xfun 0.54 (91ms)
#> ✔ Installed xtable 1.8-4 (92ms)
#> ✔ Installed yaml 2.3.11 (148ms)
#> ℹ Building BiocStyle 2.38.0
#> ✔ Installed zoo 1.8-14 (185ms)
#> ✔ Installed BiocGenerics 0.56.0 (1s)
#> ℹ Building Biobase 2.70.0
#> ✔ Packaged presto 1.0.0 (1.6s)
#> ℹ Building presto 1.0.0
#> ✔ Built BiocStyle 2.38.0 (3.3s)
#> ℹ Building S4Vectors 0.48.0
#> ✔ Built Biobase 2.70.0 (11.8s)
#> ✔ Installed Biobase 2.70.0 (72ms)
#> ✔ Installed BiocStyle 2.38.0 (50ms)
#> ✔ Installed MatrixGenerics 1.22.0 (1s)
#> ✔ Built BiocParallel 1.44.0 (18.5s)
#> ✔ Installed BiocParallel 1.44.0 (60ms)
#> ✔ Built presto 1.0.0 (21.2s)
#> ✔ Installed presto 1.0.0 (github::immunogenomics/presto@7636b3d) (40ms)
#> ✔ Built S4Vectors 0.48.0 (20.6s)
#> ✔ Installed S4Vectors 0.48.0 (49ms)
#> ℹ Building IRanges 2.44.0
#> ✔ Built IRanges 2.44.0 (35.7s)
#> ✔ Installed IRanges 2.44.0 (44ms)
#> ℹ Building S4Arrays 1.10.1
#> ℹ Building Seqinfo 1.0.0
#> ℹ Building XVector 0.50.0
#> ✔ Built Seqinfo 1.0.0 (6.6s)
#> ✔ Installed Seqinfo 1.0.0 (28ms)
#> ℹ Building GenomicRanges 1.62.0
#> ✔ Built XVector 0.50.0 (12.1s)
#> ✔ Installed XVector 0.50.0 (27ms)
#> ✔ Built S4Arrays 1.10.1 (13.9s)
#> ✔ Installed S4Arrays 1.10.1 (32ms)
#> ℹ Building SparseArray 1.10.4
#> ✔ Built GenomicRanges 1.62.0 (13.5s)
#> ✔ Installed GenomicRanges 1.62.0 (52ms)
#> ✔ Built SparseArray 1.10.4 (20.9s)
#> ✔ Installed SparseArray 1.10.4 (49ms)
#> ℹ Building DelayedArray 0.36.0
#> ✔ Built DelayedArray 0.36.0 (16s)
#> ✔ Installed DelayedArray 0.36.0 (43ms)
#> ℹ Building SummarizedExperiment 1.40.0
#> ✔ Built SummarizedExperiment 1.40.0 (14.4s)
#> ✔ Installed SummarizedExperiment 1.40.0 (43ms)
#> ℹ Building DESeq2 1.50.2
#> ℹ Building SingleCellExperiment 1.32.0
#> ✔ Built SingleCellExperiment 1.32.0 (12.9s)
#> ✔ Installed SingleCellExperiment 1.32.0 (47ms)
#> ✔ Built DESeq2 1.50.2 (29.2s)
#> ✔ Installed DESeq2 1.50.2 (1.1s)
#> ✔ 1 pkg + 177 deps: kept 8, added 170, dld 165 (NA B) [3m 20.1s]
#> Error in loadNamespace(x): there is no package called ‘CellChat’
CellChatPlot(pancreas_sub, plot_type = "aggregate")
#> Error in CellChatPlot(pancreas_sub, plot_type = "aggregate"): No CellChat results found in the Seurat object. Please run
#> `RunCellChat()` first.
CellChatPlot(pancreas_sub, plot_type = "pathway")
#> Error in CellChatPlot(pancreas_sub, plot_type = "pathway"): No CellChat results found in the Seurat object. Please run
#> `RunCellChat()` first.
CellChatPlot(pancreas_sub, plot_type = "bubble")
#> Error in CellChatPlot(pancreas_sub, plot_type = "bubble"): No CellChat results found in the Seurat object. Please run
#> `RunCellChat()` first.
CellChatPlot(pancreas_sub, plot_type = "gene")
#> Error in CellChatPlot(pancreas_sub, plot_type = "gene"): No CellChat results found in the Seurat object. Please run
#> `RunCellChat()` first.
CellChatPlot(pancreas_sub, plot_type = "heatmap")
#> Error in CellChatPlot(pancreas_sub, plot_type = "heatmap"): No CellChat results found in the Seurat object. Please run
#> `RunCellChat()` first.