This is a modified version of harmony::RunHarmony specifically designed for compatibility with RunSymphonyMap.
Usage
RunHarmony2(object, ...)
# S3 method for class 'Seurat'
RunHarmony2(
object,
group.by.vars,
assay = NULL,
reduction = "pca",
dims.use = 1:30,
project.dim = TRUE,
reduction.name = "Harmony",
reduction.key = "Harmony_",
verbose = TRUE,
seed.use = 11L,
...
)Arguments
- object
A Seurat object.
- ...
Additional arguments to be passed to harmony::RunHarmony.
- group.by.vars
The batch variable name.
- assay
The assay to be used. Default is
NULL.- reduction
The reduction to be used. Default is
"pca".- dims.use
The dimensions to be used. Default is
1:30.- project.dim
Whether to project dimension reduction loadings. Default is
TRUE.- reduction.name
The name of the reduction to be stored in the Seurat object. Default is
"Harmony".- reduction.key
The prefix for the column names of the Harmony embeddings. Default is
"Harmony_".- verbose
Whether to print the message. Default is
TRUE.- seed.use
The random seed to be used. Default is
11.
Examples
data(panc8_sub)
panc8_sub <- standard_scop(panc8_sub)
#> StandardPC_ 1
#> Positive: CHGA, PCSK1N, G6PC2, PCSK1, IAPP, ARFGEF3, CRYBA2, PRUNE2, CDKN1C, SORL1
#> EDN3, CADM1, FXYD2, ELMO1, HADH, PAPPA2, GRIA3, RBP4, DLK1, ANXA6
#> HMGN2, GNAZ, AMPD2, IGF2, ROBO2, DNAJA4, PDK4, SEPT3, CD99L2, SYT17
#> Negative: IFITM3, ZFP36L1, SOX4, ANXA4, KRT7, TPM1, PMEPA1, SERPING1, TM4SF1, CD44
#> CDC42EP1, TMSB10, NFIB, SAT1, SDC4, SPTBN1, LCN2, KRT18, PDZK1IP1, MSN
#> SMAD3, CLDN10, CFTR, NOTCH2, KRT19, CTSH, SERPINA5, FLRT2, C3, EPS8
#> StandardPC_ 2
#> Positive: SPARC, COL4A1, COL15A1, COL1A2, COL3A1, PXDN, PDGFRB, COL5A1, BGN, COL5A2
#> COL1A1, LAMA4, TIMP3, COL6A2, IGFBP4, AEBP1, SFRP2, THBS2, FBN1, COL6A1
#> CDH11, VCAN, SERPINE1, WNT5A, FN1, TPM2, FMOD, MMP2, SNAI1, DCN
#> Negative: KRT8, SPINK1, PRSS1, ELF3, GATM, MUC1, KRT18, CPA2, CTRB1, SDC4
#> PRSS3, CLDN4, LCN2, ANPEP, CPA1, PDZK1IP1, PLA2G1B, CTRC, CPB1, PNLIP
#> KLK1, CELA2A, CELA3A, KRT7, GSTA1, CD44, PNLIPRP1, PNLIPRP2, CELA3B, GSTA2
#> StandardPC_ 3
#> Positive: FTO, SORL1, TBC1D24, CASR, PCYOX1, UTRN, ADH5, ENPP5, RNF14, PHKB
#> MAP1A, C2CD5, TTC17, RAB22A, PRR14L, AP3B1, MTR, HERC1, EXPH5, SMCHD1
#> ROBO1, ABHD10, PRUNE2, SPEN, BTBD3, IBTK, ARFGEF2, TSC1, PARP4, RMND5A
#> Negative: HSPB1, CELA3A, CELA3B, CLPS, CTRB1, SYCN, CELA2A, EIF4A1, VIM, PNLIPRP1
#> PLA2G1B, KLK1, CPA1, CTRC, DDIT4, PLTP, BGN, DYNLL2, ANGPTL4, COL6A2
#> IFITM1, IGFBP4, IGFBP2, TMSB10, PRSS1, CTRL, PDGFRB, CPA2, PRSS3, PXDN
#> StandardPC_ 4
#> Positive: CPA2, PNLIP, PRSS1, CTRC, CPA1, CPB1, PLA2G1B, PNLIPRP2, PRSS3, BCAT1
#> CEL, KLK1, CELA2A, CTRB1, PNLIPRP1, SPINK1, GSTA2, MGST1, CELA3A, LDHB
#> ALB, CTRL, CELA3B, CLPS, ALDOB, REG3G, FAM129A, GSTA1, SYCN, CBS
#> Negative: CFTR, MMP7, KRT19, SERPINA5, TINAGL1, AQP1, SPP1, SERPING1, PMEPA1, KRT23
#> ALDH1A3, TSPAN8, PROM1, IGFBP7, VCAM1, LGALS4, ONECUT2, TRPV6, CCL2, ANXA3
#> TNFAIP2, CTSH, SDC1, SLC3A1, CLDN10, ANXA9, CCND1, KRT80, VNN1, PDGFD
#> StandardPC_ 5
#> Positive: COL5A1, COL1A2, COL1A1, SFRP2, COL5A2, COL3A1, VCAN, FN1, PDGFRB, THBS2
#> FMOD, BGN, ANTXR1, MXRA8, COL6A1, AEBP1, TPM2, CDH11, DCN, ISLR
#> TGFB3, COL6A2, LTBP2, DDR2, EDNRA, ANO1, LTBP1, GFPT2, WNT5A, HEYL
#> Negative: CD93, PLVAP, PODXL, ACVRL1, ESAM, S1PR1, CXCR4, ECSCR, DYSF, CALCRL
#> ADGRF5, STC1, CD34, AFAP1L1, IFI27, SH3BP5, ACKR3, ANGPT2, DLL4, MMRN2
#> MCAM, PNP, IL3RA, SPARCL1, TCF4, FAM198B, RAPGEF5, ARHGAP31, P2RY6, F2RL3
panc8_sub <- RunHarmony2(
panc8_sub,
group.by.vars = "tech",
reduction = "pca"
)
#>
#> → Will install 2 packages.
#> → All 2 packages (0 B) are cached.
#> + RhpcBLASctl 0.23-42
#> + harmony 1.2.4
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 2 pkgs are cached
#> ✔ Got RhpcBLASctl 0.23-42 (x86_64-pc-linux-gnu-ubuntu-24.04) (14.56 kB)
#> ✔ Got harmony 1.2.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.80 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:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble 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 libx11-dev libcurl4-openssl-dev libssl-dev make zlib1g-dev libglpk-dev libxml2-dev pandoc libpng-dev libfreetype6-dev libjpeg-dev libtiff-dev libwebp-dev python3 libicu-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libx11-dev is already the newest version (2:1.8.7-1build1).
#> 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).
#> pandoc is already the newest version (3.1.3+ds-2).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> libfreetype-dev is already the newest version (2.13.2+dfsg-1build3).
#> libjpeg-dev is already the newest version (8c-2ubuntu11).
#> libtiff-dev is already the newest version (4.5.1+git230720-4ubuntu2.4).
#> libwebp-dev is already the newest version (1.3.2-0.4build3).
#> 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).
#> 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 49 not upgraded.
#> ✔ Installed RhpcBLASctl 0.23-42 (36ms)
#> ✔ Installed harmony 1.2.4 (102ms)
#> ✔ 1 pkg + 200 deps: kept 199, added 2, dld 2 (4.81 MB) [8.7s]
#> Transposing data matrix
#> Initializing state using k-means centroids initialization
#> Harmony 1/10
#> Harmony 2/10
#> Harmony 3/10
#> Harmony 4/10
#> Harmony 5/10
#> Harmony 6/10
#> Harmony 7/10
#> Harmony converged after 7 iterations
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "pca"
)
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "Harmony"
)
panc8_sub <- standard_scop(
panc8_sub,
prefix = "Harmony",
linear_reduction = "Harmony"
)
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "StandardpcaUMAP2D"
)
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "HarmonyUMAP2D"
)
