Run DM (diffusion map)
Usage
RunDM(object, ...)
# S3 method for class 'Seurat'
RunDM(
object,
reduction = "pca",
dims = 1:30,
features = NULL,
assay = NULL,
layer = "data",
ndcs = 2,
sigma = "local",
k = 30,
dist.method = "euclidean",
reduction.name = "dm",
reduction.key = "DM_",
verbose = TRUE,
seed.use = 11,
...
)
# Default S3 method
RunDM(
object,
assay = NULL,
layer = "data",
ndcs = 2,
sigma = "local",
k = 30,
dist.method = "euclidean",
reduction.key = "DM_",
verbose = TRUE,
seed.use = 11,
...
)Arguments
- object
An object. This can be a Seurat object or a matrix-like object.
- ...
Additional arguments to be passed to destiny::DiffusionMap.
- reduction
The reduction to be used. Default is
"pca".- dims
The dimensions to be used. Default is
1:30.- features
The features to be used. Default is
NULL.- assay
The assay to be used. Default is
NULL.- layer
The layer to be used. Default is
"data".- ndcs
A number of diffusion components (dimensions) to be computed. Default is
2.- sigma
The diffusion scale parameter of the Gaussian kernel. Currently supported values are
"local"(default) and"global".- k
A number of nearest neighbors to be used for the construction of the graph. Default is
30.- dist.method
The distance metric to be used for the construction of the knn graph. Currently supported values are
"euclidean"and"cosine". Default is"euclidean".- reduction.name
The name of the reduction to be stored in the Seurat object. Default is
"dm".- reduction.key
The prefix for the column names of the basis vectors. Default is
"DM_".- verbose
Whether to print the message. Default is
TRUE.- seed.use
An integer specifying the random seed to be used. Default is
11.
Examples
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2025-11-13 12:14:13] Start standard scop workflow...
#> ℹ [2025-11-13 12:14:14] Checking a list of <Seurat> object...
#> ! [2025-11-13 12:14:14] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2025-11-13 12:14:14] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2025-11-13 12:14:17] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2025-11-13 12:14:17] Use the separate HVF from srt_list
#> ℹ [2025-11-13 12:14:17] Number of available HVF: 2000
#> ℹ [2025-11-13 12:14:17] Finished check
#> ℹ [2025-11-13 12:14:18] Perform `Seurat::ScaleData()`
#> ℹ [2025-11-13 12:14:18] 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 12:14:19] Perform `Seurat::FindClusters()` with louvain and `cluster_resolution` = 0.6
#> ℹ [2025-11-13 12:14:19] Reorder clusters...
#> ℹ [2025-11-13 12:14:19] Perform umap nonlinear dimension reduction
#> ℹ [2025-11-13 12:14:19] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-11-13 12:14:19] UMAP will return its model
#> ℹ [2025-11-13 12:14:24] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-11-13 12:14:24] UMAP will return its model
#> ✔ [2025-11-13 12:14:29] Run scop standard workflow done
pancreas_sub <- RunDM(
object = pancreas_sub,
features = SeuratObject::VariableFeatures(pancreas_sub)
)
#> ◌ [2025-11-13 12:14:29] Installing: destiny...
#>
#> → Will install 18 packages.
#> → All 18 packages (0 B) are cached.
#> + DEoptimR 1.1-4
#> + RcppHNSW 0.6.0
#> + TTR 0.24.4
#> + VIM 6.2.6
#> + destiny 3.24.0 [bld][cmp]
#> + ggplot.multistats 1.0.1
#> + ggthemes 5.1.0
#> + knn.covertree 1.0
#> + laeken 0.5.3
#> + lmtest 0.9-40
#> + pcaMethods 2.2.0 [bld][cmp]
#> + ranger 0.17.0
#> + robustbase 0.99-6
#> + smoother 1.3
#> + sp 2.2-0
#> + vcd 1.4-13
#> + xts 0.14.1
#> + zoo 1.8-14
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 18 pkgs are cached
#> ✔ Got destiny 3.24.0 (source) (900.68 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 libcurl4-openssl-dev libssl-dev make cmake libicu-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).
#> cmake is already the newest version (3.28.3-1build7).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
#> ℹ Building pcaMethods 2.2.0
#> ✔ Installed DEoptimR 1.1-4 (113ms)
#> ✔ Installed ggplot.multistats 1.0.1 (116ms)
#> ✔ Installed ggthemes 5.1.0 (187ms)
#> ✔ Installed knn.covertree 1.0 (77ms)
#> ✔ Installed laeken 0.5.3 (77ms)
#> ✔ Installed lmtest 0.9-40 (74ms)
#> ✔ Installed ranger 0.17.0 (84ms)
#> ✔ Installed RcppHNSW 0.6.0 (90ms)
#> ✔ Installed robustbase 0.99-6 (80ms)
#> ✔ Installed smoother 1.3 (114ms)
#> ✔ Installed sp 2.2-0 (120ms)
#> ✔ Installed TTR 0.24.4 (77ms)
#> ✔ Installed vcd 1.4-13 (77ms)
#> ✔ Installed VIM 6.2.6 (87ms)
#> ✔ Installed xts 0.14.1 (82ms)
#> ✔ Installed zoo 1.8-14 (53ms)
#> ✔ Built pcaMethods 2.2.0 (9s)
#> ✔ Installed pcaMethods 2.2.0 (39ms)
#> ℹ Building destiny 3.24.0
#> ✔ Built destiny 3.24.0 (29.1s)
#> ✔ Installed destiny 3.24.0 (54ms)
#> ✔ 1 pkg + 103 deps: kept 86, added 18, dld 1 (900.68 kB) [45.1s]
#> ✔ [2025-11-13 12:15:14] destiny installed successfully
#> finding knns......done. Time: 15.75s
#> Calculating transition probabilities......done. Time: 0.01s
#>
#> 'as(<dsCMatrix>, "dgTMatrix")' is deprecated.
#> Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead.
#> See help("Deprecated") and help("Matrix-deprecated").
#> performing eigen decomposition......done. Time: 0.01s
CellDimPlot(
pancreas_sub,
group.by = "CellType",
reduction = "dm"
)
