Run DM (diffusion map)

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)
#> 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 
pancreas_sub <- RunDM(
  object = pancreas_sub,
  features = SeuratObject::VariableFeatures(pancreas_sub)
)
#>  
#> → Will install 18 packages.
#> → All 18 packages (0 B) are cached.
#> + DEoptimR            1.1-4  
#> + VIM                 6.2.6  
#> + destiny             3.24.0 [bld][cmp]
#> + e1071               1.7-16 
#> + ggplot.multistats   1.0.1  
#> + ggthemes            5.2.0  
#> + knn.covertree       1.0    
#> + laeken              0.5.3  
#> + org.Mm.eg.db        3.22.0 [bld]
#> + pcaMethods          2.2.0  [bld][cmp]
#> + proxy               0.4-27 
#> + ranger              0.17.0 
#> + repr                1.1.7  
#> + rgl                 1.3.31  + ✔ libfreetype6-dev, ✖ libglu1-mesa-dev, ✖ texlive, ✔ libpng-dev, ✖ libgl1-mesa-dev, ✔ pandoc, ✔ zlib1g-dev
#> + robustbase          0.99-6 
#> + scatterplot3d       0.3-44 
#> + smoother            1.3    
#> + vcd                 1.4-13 
#> → Will install 3 system packages:
#> + libgl1-mesa-dev   - rgl
#> + libglu1-mesa-dev  - rgl
#> + texlive           - rgl
#> ℹ No downloads are needed, 18 pkgs are cached
#> ✔ Got e1071 1.7-16 (x86_64-pc-linux-gnu-ubuntu-24.04) (596.57 kB)
#> ✔ Got DEoptimR 1.1-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (74.64 kB)
#> ✔ Got smoother 1.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (22.69 kB)
#> ✔ Got destiny 3.24.0 (source) (900.68 kB)
#> ✔ Got proxy 0.4-27 (x86_64-pc-linux-gnu-ubuntu-24.04) (175.47 kB)
#> ✔ Got pcaMethods 2.2.0 (source) (1.05 MB)
#> ✔ Got ranger 0.17.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (473.78 kB)
#> ✔ Got knn.covertree 1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (91.51 kB)
#> ✔ Got ggthemes 5.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (969.47 kB)
#> ✔ Got ggplot.multistats 1.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (31.64 kB)
#> ✔ Got laeken 0.5.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.16 MB)
#> ✔ Got scatterplot3d 0.3-44 (x86_64-pc-linux-gnu-ubuntu-24.04) (348.15 kB)
#> ✔ Got VIM 6.2.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.77 MB)
#> ✔ Got vcd 1.4-13 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.30 MB)
#> ✔ Got repr 1.1.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (128.02 kB)
#> ✔ Got robustbase 0.99-6 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.13 MB)
#> ✔ Got rgl 1.3.31 (x86_64-pc-linux-gnu-ubuntu-24.04) (6.45 MB)
#> ✔ Got org.Mm.eg.db 3.22.0 (source) (92.82 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
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#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libfreetype6-dev libglu1-mesa-dev texlive libpng-dev libgl1-mesa-dev pandoc zlib1g-dev make libcurl4-openssl-dev libnode-dev libxml2-dev libx11-dev libssl-dev libglpk-dev cmake libjpeg-dev libtiff-dev libwebp-dev libicu-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev`
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#> cmake is already the newest version (3.28.3-1build7).
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#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> libfontconfig1-dev is already the newest version (2.15.0-1.1ubuntu2).
#> libfribidi-dev is already the newest version (1.0.13-3build1).
#> libharfbuzz-dev is already the newest version (8.3.0-2build2).
#> The following additional packages will be installed:
#>   dvisvgm fonts-lmodern fonts-texgyre fonts-texgyre-math libegl-dev
#>   libegl-mesa0 libegl1 libgl-dev libgles-dev libgles1 libgles2 libglu1-mesa
#>   libglvnd-core-dev libglvnd-dev libglx-dev libgumbo2 libkpathsea6 libmujs3
#> libopengl-dev libopengl0 libpotrace0 libptexenc1 libsynctex2 libteckit0
#>   libtexlua53-5 libwoff1 libzzip-0-13t64 lmodern mupdf-tools tex-gyre
#>   texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base
#>   texlive-latex-recommended tipa
#> Suggested packages:
#>   perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview
#>   texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex
#>   texlive-latex-recommended-doc texlive-luatex texlive-pstricks tipa-doc
#> The following NEW packages will be installed:
#>   dvisvgm fonts-lmodern fonts-texgyre fonts-texgyre-math libegl-dev
#>   libegl-mesa0 libegl1 libgl-dev libgl1-mesa-dev libgles-dev libgles1 libgles2
#>   libglu1-mesa libglu1-mesa-dev libglvnd-core-dev libglvnd-dev libglx-dev
#> libgumbo2 libkpathsea6 libmujs3 libopengl-dev libopengl0 libpotrace0
#>   libptexenc1 libsynctex2 libteckit0 libtexlua53-5 libwoff1 libzzip-0-13t64
#>   lmodern mupdf-tools tex-gyre texlive texlive-base texlive-binaries
#>   texlive-fonts-recommended texlive-latex-base texlive-latex-recommended tipa
#> 0 upgraded, 39 newly installed, 0 to remove and 49 not upgraded.
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CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "dm"
)