MSC analysis of single-cell transcriptome of breast cancer

This is the R script used to reproduce Figure 6 of the MSC manuscript to analyze breast cancer scRNA-seq from Wu et al. 2021. The pre-processed data by Seurat workflow (integrated_data.seurat_wt_celltype.RDS), SNN-based results (SNN.clusters.RDS), MSC results (Flu.MSC_results.RDS) and codes for evaluation metric (evaluation_functions.R) can be downloaded from Synpase with DOI, https://doi.org/10.7303/syn52966803, under ‘Wu_et_al_2021’ folder. Placing these files under the working directory will run the codes below.

Section 1. Loading data

rm(list = ls())

library(Seurat)
## Loading required package: SeuratObject
## Loading required package: sp
## 
## Attaching package: 'SeuratObject'
## The following objects are masked from 'package:base':
## 
##     intersect, t
library(Matrix.utils)
## Loading required package: Matrix
library(Matrix)
library(doParallel)
## Loading required package: foreach
## Loading required package: iterators
## Loading required package: parallel
library(igraph)
## 
## Attaching package: 'igraph'
## The following object is masked from 'package:Seurat':
## 
##     components
## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum
## The following object is masked from 'package:base':
## 
##     union
library(ggraph)
## Loading required package: ggplot2
## 
## Attaching package: 'ggraph'
## The following object is masked from 'package:sp':
## 
##     geometry
library(MSC)
library(cowplot)

root.dir = "/media/won-min/My Passport1/SingleCell/Cancer/Breast/Wu_et_al_2021"
setwd(root.dir)

# load functions
if (file.exists("evaluation_functions.R")) source("evaluation_functions.R")
if (file.exists("enrichment_functions.v3.R")) source("enrichment_functions.v3.R")

seu = readRDS(file = "Breast_Wu.NG.2021.Singlet.RPCA_CCA_updated_wt_SCT.rds")

Section 2. UMAP plots of cell types and MSC results

## Loading required package: RColorBrewer
## Loading required package: grid
## Warning: ggrepel: 12 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

Section 3. Cell type detection performance metrics

## 
## Attaching package: 'patchwork'
## The following object is masked from 'package:cowplot':
## 
##     align_plots
## Loading required package: reshape
## 
## Attaching package: 'reshape'
## The following object is masked from 'package:cowplot':
## 
##     stamp
## The following object is masked from 'package:Matrix':
## 
##     expand
## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by
## the caller; using TRUE

## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by
## the caller; using TRUE

## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by
## the caller; using TRUE

## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by
## the caller; using TRUE

## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by
## the caller; using TRUE

## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by
## the caller; using TRUE
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.4' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.8' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.4' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.4' in 'mbcsToSbcs': dot substituted for <b3>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.8' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.8' in 'mbcsToSbcs': dot substituted for <b3>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=1.2' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=1.2' in 'mbcsToSbcs': dot substituted for <b3>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.4' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.4' in 'mbcsToSbcs': dot substituted for <b3>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.8' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=0.8' in 'mbcsToSbcs': dot substituted for <b3>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=1.2' in 'mbcsToSbcs': dot substituted for <ce>
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'SNN γ=1.2' in 'mbcsToSbcs': dot substituted for <b3>

## Section 4. Pie chart visualization of MSC clusters

## Loading required package: reshape2
## 
## Attaching package: 'reshape2'
## The following objects are masked from 'package:reshape':
## 
##     colsplit, melt, recast
## $M227
## 
##         T_cells_c0_CD4+_CCR7         T_cells_c1_CD4+_IL7R 
##                          320                          447 
## T_cells_c2_CD4+_T-regs_FOXP3   T_cells_c3_CD4+_Tfh_CXCL13 
##                            2                            3 
##        T_cells_c4_CD8+_ZFP36         T_cells_c5_CD8+_GZMK 
##                           12                            3 
##             T_cells_c6_IFIT1     T_cells_c9_NK_cells_AREG 
##                           39                            1 
## 
## $M180
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                  20                  25                 159                 341 
##      Cancer LumB SC Luminal Progenitors      Mature Luminal 
##                 111                   1                  61 
## 
## $M226
## 
##              Cancer Basal SC         T_cells_c0_CD4+_CCR7 
##                            1                          133 
##         T_cells_c1_CD4+_IL7R            T_cells_c11_MKI67 
##                          346                            2 
## T_cells_c2_CD4+_T-regs_FOXP3   T_cells_c3_CD4+_Tfh_CXCL13 
##                           32                           65 
##        T_cells_c4_CD8+_ZFP36         T_cells_c5_CD8+_GZMK 
##                           10                            2 
##             T_cells_c6_IFIT1         T_cells_c7_CD8+_IFNG 
##                           30                            5 
##         T_cells_c8_CD8+_LAG3 
##                            2 
## 
## $M235
## 
##              B cells Memory       CAFs MSC iCAF-like s2 
##                           1                           1 
##             Cancer Basal SC              Cancer Cycling 
##                         126                          40 
##              Cancer Her2 SC              Cancer LumA SC 
##                          86                         168 
##              Cancer LumB SC Endothelial Lymphatic LYVE1 
##                         134                           1 
##         Luminal Progenitors              Mature Luminal 
##                          13                           7 
##               Myoepithelial       PVL Differentiated s3 
##                           1                           3 
## 
## $M237
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                  57                  22                  84                 224 
##      Cancer LumB SC Luminal Progenitors      Mature Luminal 
##                 162                  16                   8 
## 
## $M234
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                 195                  89                 118                  47 
##      Cancer LumB SC Luminal Progenitors      Mature Luminal 
##                  43                   4                   9 
## 
## $M196
## 
##         T_cells_c0_CD4+_CCR7         T_cells_c1_CD4+_IL7R 
##                            2                           29 
## T_cells_c10_NKT_cells_FCGR3A            T_cells_c11_MKI67 
##                           22                           24 
##   T_cells_c3_CD4+_Tfh_CXCL13        T_cells_c4_CD8+_ZFP36 
##                            1                           93 
##         T_cells_c5_CD8+_GZMK             T_cells_c6_IFIT1 
##                            9                           18 
##         T_cells_c7_CD8+_IFNG         T_cells_c8_CD8+_LAG3 
##                          242                           56 
##     T_cells_c9_NK_cells_AREG 
##                            3 
## 
## $M240
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                  12                  19                  83                 216 
##      Cancer LumB SC Luminal Progenitors      Mature Luminal 
##                  41                   1                  42 
## 
## $M181
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                  40                  26                  78                 186 
##      Cancer LumB SC Luminal Progenitors      Mature Luminal 
##                  70                   1                  12 
## 
## $M103
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                 121                 140                  44                  17 
##      Cancer LumB SC Luminal Progenitors      Mature Luminal 
##                  13                  10                   5 
## 
## $M203
## 
## Endothelial ACKR1 
##               323 
## 
## $M144
## 
## CAFs MSC iCAF-like s2       Cancer Basal SC        Cancer LumA SC 
##                     1                     2                     1 
##           Cycling PVL PVL Differentiated s3       PVL Immature s1 
##                     2                   274                     3 
##       PVL_Immature s2 
##                     1 
## 
## $M121
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                   209                    13                     9 
##    CAFs myCAF like s5 CAFs Transitioning s3 
##                     3                    23 
## 
## $M145
## 
##           Cycling PVL PVL Differentiated s3       PVL Immature s1 
##                     2                   243                     9 
##       PVL_Immature s2 
##                     3 
## 
## $M102
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     2                     4                    22 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                     4                     1                    88 
##        Cancer Cycling        Cancer Her2 SC        Cancer LumA SC 
##                    40                    25                     6 
##        Cancer LumB SC           Cycling PVL   Luminal Progenitors 
##                     2                     1                     4 
##        Mature Luminal         Myoepithelial PVL Differentiated s3 
##                     2                    41                    10 
##       PVL Immature s1       PVL_Immature s2 
##                     2                     2 
## 
## $M146
## 
## CAFs MSC iCAF-like s2       Cancer Basal SC           Cycling PVL 
##                     2                     2                     1 
## PVL Differentiated s3 
##                   248 
## 
## $M188
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     5                     9                    25 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                   185                    13                    13 
##        Cancer Cycling 
##                     1 
## 
## $M133
## 
##              Cancer LumB SC           Endothelial ACKR1 
##                           1                          87 
##          Endothelial CXCL12 Endothelial Lymphatic LYVE1 
##                          75                           3 
##            Endothelial RGS5 
##                          79 
## 
## $M244
## 
##                 B cells Memory          Myeloid_c1_LAM1_FABP5 
##                              2                             58 
##  Myeloid_c10_Macrophage_1_EGR1    Myeloid_c12_Monocyte_1_IL1B 
##                            140                             37 
##           Myeloid_c2_LAM2_APOE Myeloid_c9_Macrophage_2_CXCL10 
##                              2                              3 
## 
## $M119
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     2                    14                    64 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                    55                     4                    69 
##        Cancer Cycling        Cancer Her2 SC        Cancer LumA SC 
##                    21                     1                     1 
## PVL Differentiated s3       PVL Immature s1 
##                     2                     2 
## 
## $M212
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     1                    24                    39 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                     5                     1                    12 
##        Cancer Cycling           Cycling PVL PVL Differentiated s3 
##                     3                     1                     7 
##       PVL Immature s1       PVL_Immature s2 
##                    70                    72 
## 
## $M108
## 
##       Cancer Cycling    T_cells_c11_MKI67 T_cells_c8_CD8+_LAG3 
##                  189                   29                    1 
## 
## $M252
## 
##                 B cells Memory          Myeloid_c1_LAM1_FABP5 
##                              1                             88 
##  Myeloid_c10_Macrophage_1_EGR1    Myeloid_c12_Monocyte_1_IL1B 
##                             98                             12 
##           Myeloid_c2_LAM2_APOE Myeloid_c9_Macrophage_2_CXCL10 
##                              6                              2 
## 
## $M222
## 
##                Cycling_Myeloid            Myeloid_c0_DC_LAMP3 
##                              2                              2 
##          Myeloid_c1_LAM1_FABP5  Myeloid_c10_Macrophage_1_EGR1 
##                             47                             45 
##          Myeloid_c11_cDC2_CD1C    Myeloid_c12_Monocyte_1_IL1B 
##                              1                             56 
##           Myeloid_c2_LAM2_APOE Myeloid_c9_Macrophage_2_CXCL10 
##                              8                             42 
## 
## $M241
## 
## Cancer Basal SC  Cancer Cycling  Cancer Her2 SC  Cancer LumA SC  Cancer LumB SC 
##               8               4              28              81              62 
##  Mature Luminal 
##              15 
## 
## $M142
## 
## PVL Differentiated s3 
##                   194 
## 
## $M138
## 
##  Endothelial ACKR1 Endothelial CXCL12   Endothelial RGS5 
##                 77                 72                 38 
## 
## $M192
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                    10                     2                     1 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                   131                    38                     3 
## 
## $M246
## 
##                Cycling_Myeloid          Myeloid_c1_LAM1_FABP5 
##                             24                             37 
##  Myeloid_c10_Macrophage_1_EGR1          Myeloid_c11_cDC2_CD1C 
##                             19                              2 
##    Myeloid_c12_Monocyte_1_IL1B           Myeloid_c2_LAM2_APOE 
##                             39                             50 
##         Myeloid_c3_cDC1_CLEC9A        Myeloid_c4_DCs_pDC_IRF7 
##                              1                              1 
## Myeloid_c9_Macrophage_2_CXCL10 
##                             11 
## 
## $M214
## 
## CAFs MSC iCAF-like s2       Cancer Basal SC           Cycling PVL 
##                     1                     2                     1 
## PVL Differentiated s3 
##                   176 
## 
## $M190
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     7                    18                    40 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                    73                    27                    10 
##        Cancer LumB SC 
##                     1 
## 
## $M230
## 
##       T_cells_c1_CD4+_IL7R          T_cells_c11_MKI67 
##                          2                         19 
## T_cells_c3_CD4+_Tfh_CXCL13       T_cells_c8_CD8+_LAG3 
##                        144                          3 
## 
## $M191
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                    59                     2                     3 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                    32                    55                     1 
## 
## $M150
## 
##     Cancer Basal SC      Cancer Cycling      Cancer Her2 SC      Cancer LumA SC 
##                  54                  71                   3                   1 
## Luminal Progenitors      Mature Luminal       Myoepithelial 
##                   4                   1                  17 
## 
## $M187
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                    38                    14                    23 
##    CAFs myCAF like s5 CAFs Transitioning s3 
##                    45                    31 
## 
## $M162
## 
##                 B cells Memory                Cycling_Myeloid 
##                              2                              3 
##          Myeloid_c1_LAM1_FABP5  Myeloid_c10_Macrophage_1_EGR1 
##                             25                              8 
##          Myeloid_c11_cDC2_CD1C    Myeloid_c12_Monocyte_1_IL1B 
##                              7                             58 
##           Myeloid_c2_LAM2_APOE   Myeloid_c7_Monocyte_3_FCGR3A 
##                             16                              1 
##   Myeloid_c8_Monocyte_2_S100A9 Myeloid_c9_Macrophage_2_CXCL10 
##                             29                              1 
## 
## $M143
## 
## CAFs MSC iCAF-like s2       Cancer Basal SC        Cancer Her2 SC 
##                     1                     1                     1 
## PVL Differentiated s3       PVL Immature s1       PVL_Immature s2 
##                   126                    11                     3 
## 
## $M233
## 
##          T_cells_c11_MKI67 T_cells_c3_CD4+_Tfh_CXCL13 
##                          1                        140 
##       T_cells_c8_CD8+_LAG3 
##                          1 
## 
## $M111
## 
##   Cancer Basal SC    Cancer Cycling    Cancer Her2 SC    Cancer LumA SC 
##                 1               128                 2                 2 
##   Cycling_Myeloid T_cells_c11_MKI67 
##                 1                 5 
## 
## $M152
## 
## Cancer Basal SC  Cancer Cycling  Cancer Her2 SC  Cancer LumB SC   Myoepithelial 
##              87              37               1               1              11 
## 
## $M149
## 
## Cancer Basal SC  Cancer Cycling  Cancer Her2 SC   Myoepithelial 
##              84              34               1              14 
## 
## $M243
## 
## CAFs MSC iCAF-like s2    CAFs myCAF like s4    CAFs myCAF like s5 
##                     6                    12                    97 
## CAFs Transitioning s3       Cancer Basal SC        Cancer Cycling 
##                     3                    11                     1 
## 
## $M189
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                    11                     6                    30 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                    58                    15                     6 
## 
## $M242
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     5                     3                    13 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                    88                    10                     2 
## 
## $M251
## 
##          Myeloid_c1_LAM1_FABP5  Myeloid_c10_Macrophage_1_EGR1 
##                             25                             54 
##    Myeloid_c12_Monocyte_1_IL1B           Myeloid_c2_LAM2_APOE 
##                              7                             20 
## Myeloid_c9_Macrophage_2_CXCL10 
##                             12 
## 
## $M231
## 
##            T_cells_c11_MKI67 T_cells_c2_CD4+_T-regs_FOXP3 
##                            3                           36 
##   T_cells_c3_CD4+_Tfh_CXCL13 
##                           74 
## 
## $M253
## 
##                Cycling_Myeloid          Myeloid_c1_LAM1_FABP5 
##                              1                             39 
##  Myeloid_c10_Macrophage_1_EGR1    Myeloid_c12_Monocyte_1_IL1B 
##                             55                              6 
##           Myeloid_c2_LAM2_APOE Myeloid_c9_Macrophage_2_CXCL10 
##                              2                              6 
## 
## $M239
## 
## Cancer Cycling Cancer Her2 SC Cancer LumA SC Cancer LumB SC Mature Luminal 
##              2             48             44              8              4 
## 
## $M153
## 
## Cancer Basal SC  Cancer Cycling  Cancer Her2 SC   Myoepithelial 
##              77              16               1               6 
## 
## $M201
## 
##               Cancer Her2 SC         T_cells_c1_CD4+_IL7R 
##                            1                            1 
## T_cells_c10_NKT_cells_FCGR3A        T_cells_c4_CD8+_ZFP36 
##                           48                            1 
##         T_cells_c7_CD8+_IFNG     T_cells_c9_NK_cells_AREG 
##                            2                           44 
## 
## $M98
## 
## Cancer Basal SC  Cancer Cycling  Cancer Her2 SC  Cancer LumA SC  Cancer LumB SC 
##              32               7              16               9              24 
## 
## $M249
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                     4                     3                     9 
##    CAFs myCAF like s5 CAFs Transitioning s3       Cancer Basal SC 
##                    56                    10                     2 
## 
## $M77
## 
## Cancer Cycling 
##             81 
## 
## $M157
## 
## Myoepithelial 
##            78 
## 
## $M213
## 
## CAFs MSC iCAF-like s2 PVL Differentiated s3 
##                     1                    72 
## 
## $M206
## 
## Endothelial CXCL12   Endothelial RGS5 
##                 67                  1 
## 
## $M96
## 
## Plasmablasts 
##           63 
## 
## $M175
## 
## Cancer Basal SC  Cancer Cycling  Cancer Her2 SC  Cancer LumA SC    Plasmablasts 
##              42              16               1               1               1 
## 
## $M186
## 
## CAFs MSC iCAF-like s1 CAFs MSC iCAF-like s2    CAFs myCAF like s4 
##                    10                     9                     6 
##    CAFs myCAF like s5 CAFs Transitioning s3 
##                    18                    12 
## 
## $M151
## 
##     Cancer Basal SC      Cancer Cycling Luminal Progenitors       Myoepithelial 
##                  27                  21                   3                   3 
## 
## $M198
## 
##           Cancer Cycling     T_cells_c1_CD4+_IL7R        T_cells_c11_MKI67 
##                        1                        1                       42 
##    T_cells_c4_CD8+_ZFP36 T_cells_c9_NK_cells_AREG 
##                        1                        8
## Warning: `graph.data.frame()` was deprecated in igraph 2.0.0.
## ℹ Please use `graph_from_data_frame()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## 
## Attaching package: 'scatterpie'
## The following object is masked from 'package:sp':
## 
##     recenter
## Warning: Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: ggrepel: 22 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

## [Section 5. Visualize M138, a endothelial subset uniquely identified by MSC]

## Minimum UMI unchanged. Skipping re-correction.
## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
## To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
## This message will be shown once per session
## 23:04:04 UMAP embedding parameters a = 0.9922 b = 1.112
## 23:04:04 Read 6360 rows and found 8 numeric columns
## 23:04:04 Using Annoy for neighbor search, n_neighbors = 30
## 23:04:04 Building Annoy index with metric = cosine, n_trees = 50
## 0%   10   20   30   40   50   60   70   80   90   100%
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## 23:04:04 Writing NN index file to temp file /tmp/RtmpmNCmpJ/file323ee7e850
## 23:04:04 Searching Annoy index using 1 thread, search_k = 3000
## 23:04:06 Annoy recall = 100%
## 23:04:06 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 23:04:07 Initializing from normalized Laplacian + noise (using RSpectra)
## 23:04:07 Commencing optimization for 500 epochs, with 267976 positive edges
## 23:04:12 Optimization finished
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.