In [1]:
library(ArchR)
library(here)
library(Seurat)
library(SeuratDisk)
library(SingleCellExperiment)
options(repr.plot.width=15, repr.plot.height=11)
## add general functions at the top of the R scripts
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
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\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
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/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues
Loading Required Packages...
Loading Package : grid v4.3.1
Loading Package : gridExtra v2.3
Loading Package : gtools v3.9.4
Loading Package : gtable v0.3.4
Loading Package : ggplot2 v3.5.0
Warning message:
“package ‘ggplot2’ was built under R version 4.3.2”
Loading Package : magrittr v2.0.3
Loading Package : plyr v1.8.9
Loading Package : stringr v1.5.1
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Loading Package : S4Vectors v0.40.2
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Loading Package : GenomicRanges v1.54.1
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Loading Package : rhdf5 v2.42.1
here() starts at /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq
Attaching package: ‘here’
The following object is masked from ‘package:plyr’:
here
Loading required package: SeuratObject
Loading required package: sp
Warning message:
“package ‘sp’ was built under R version 4.3.2”
Attaching package: ‘sp’
The following object is masked from ‘package:IRanges’:
%over%
Attaching package: ‘SeuratObject’
The following object is masked from ‘package:SummarizedExperiment’:
Assays
The following object is masked from ‘package:GenomicRanges’:
intersect
The following object is masked from ‘package:GenomeInfoDb’:
intersect
The following object is masked from ‘package:IRanges’:
intersect
The following object is masked from ‘package:S4Vectors’:
intersect
The following object is masked from ‘package:BiocGenerics’:
intersect
The following object is masked from ‘package:base’:
intersect
Attaching package: ‘Seurat’
The following object is masked from ‘package:SummarizedExperiment’:
Assays
Registered S3 method overwritten by 'SeuratDisk':
method from
as.sparse.H5Group Seurat
In [2]:
#archr settings
addArchRGenome("mm10")
addArchRThreads(threads = 8)
Setting default genome to Mm10. Setting default number of Parallel threads to 8.
In [3]:
PROJNAME = "BICCN_mouse_Str_snATAC2_MSN"
PROJPATH = here(here("data/tidy_data/ArchRProjects"),PROJNAME) #subset proj name
PROJPATH
proj = loadArchRProject(PROJPATH)
'/projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq/data/tidy_data/ArchRProjects/BICCN_mouse_Str_snATAC2_MSN'
Successfully loaded ArchRProject!
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\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
In [4]:
p <- plotEmbedding( ArchRProj = proj, colorBy = "cellColData", name = c('Sample', 'SubRegion', 'ClustersX330'), embedding = "UMAPH330")
p3 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme(axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-69a94856ba84-Date-2024-03-20_Time-17-55-18.832757.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-69a94856ba84-Date-2024-03-20_Time-17-55-18.832757.log Warning message: “The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as of ggplot2 3.3.4.”
In [5]:
markMSN1 = c('Drd1','Tac1', 'Pdyn', 'Drd2','Adora2a','Penk') # D1 & D2 markers
# D1 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN1, embedding = "UMAPH330", imputeWeights = NULL) #
p1 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) +
theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p1))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-69a97f154fc1-Date-2024-03-20_Time-17-56-28.318016.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2024-03-20 17:56:28.690296 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-69a97f154fc1-Date-2024-03-20_Time-17-56-28.318016.log
In [6]:
markMSN2 = c('Drd1', 'Drd2', 'Foxp2', 'Grm8','Tshz1', 'Drd3')# eSPN, D1/D2, IC markers
# D2 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN2, embedding = "UMAPH330", imputeWeights = NULL)
p2 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p2))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-69a93f088b5d-Date-2024-03-20_Time-17-57-12.553345.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2024-03-20 17:57:13.002568 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-69a93f088b5d-Date-2024-03-20_Time-17-57-12.553345.log
In [19]:
## make the plots
cols1 = setNames(RColorBrewer::brewer.pal(8,'Paired')[c(2,4,6,8)], c('D1', 'eSPN', 'D2', 'IC'))
cols2 = setNames(RColorBrewer::brewer.pal(7,'Paired'),
c('D1-Matrix', 'D1-Striosome', 'D1-NUDAP', 'D1/D2H', 'D2-Matrix', 'D2-Striosome', 'IC'))
cols = c(cols1, cols2)
p <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = c('integrated_clusters', 'integrated_subclusters'),
embedding = "UMAPH330", pal = cols)
p2 <- lapply(p, function(x){
x + theme_ArchR(baseSize = 12) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank(),
legend.text=element_text(size= 12)) +
guides(color = guide_legend(override.aes = list(size=5)))
})
do.call(cowplot::plot_grid, c(list(ncol = 2),p2))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-69a977784e28-Date-2024-03-20_Time-18-05-55.974125.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-69a977784e28-Date-2024-03-20_Time-18-05-55.974125.log
In [39]:
markerGenes <- c( "Drd1", "Drd2", "Drd3", "Foxp2", 'Tshz1')
p <- plotBrowserTrack(
ArchRProj = proj, groupBy = "integrated_clusters", geneSymbol = markerGenes, pal = cols,
upstream = 500000, downstream = 500000)
ArchR logging to : ArchRLogs/ArchR-plotBrowserTrack-69a92250cc8-Date-2024-03-20_Time-18-16-53.838136.log If there is an issue, please report to github with logFile! 2024-03-20 18:16:54.109936 : Validating Region, 0.005 mins elapsed.
GRanges object with 5 ranges and 2 metadata columns:
seqnames ranges strand | gene_id symbol
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr13 54051183-54055658 - | 13488 Drd1
[2] chr9 49340662-49407214 + | 13489 Drd2
[3] chr16 43762221-43822932 + | 13490 Drd3
[4] chr6 14901349-15441977 + | 114142 Foxp2
[5] chr18 84011627-84086562 - | 110796 Tshz1
-------
seqinfo: 21 sequences from mm10 genome
2024-03-20 18:16:54.227037 : Adding Bulk Tracks (1 of 5), 0.007 mins elapsed. 2024-03-20 18:17:06.332072 : Adding Gene Tracks (1 of 5), 0.208 mins elapsed. 2024-03-20 18:17:07.614129 : Plotting, 0.23 mins elapsed. 2024-03-20 18:17:09.752565 : Adding Bulk Tracks (2 of 5), 0.265 mins elapsed. 2024-03-20 18:17:17.015864 : Adding Gene Tracks (2 of 5), 0.386 mins elapsed. 2024-03-20 18:17:19.02702 : Plotting, 0.42 mins elapsed. 2024-03-20 18:17:21.036778 : Adding Bulk Tracks (3 of 5), 0.453 mins elapsed. 2024-03-20 18:17:28.052652 : Adding Gene Tracks (3 of 5), 0.57 mins elapsed. 2024-03-20 18:17:28.272922 : Plotting, 0.574 mins elapsed. 2024-03-20 18:17:30.681391 : Adding Bulk Tracks (4 of 5), 0.614 mins elapsed. 2024-03-20 18:17:41.507341 : Adding Gene Tracks (4 of 5), 0.795 mins elapsed. 2024-03-20 18:17:41.725429 : Plotting, 0.798 mins elapsed. 2024-03-20 18:17:44.125337 : Adding Bulk Tracks (5 of 5), 0.838 mins elapsed. 2024-03-20 18:17:52.760377 : Adding Gene Tracks (5 of 5), 0.982 mins elapsed. 2024-03-20 18:17:52.982134 : Plotting, 0.986 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-plotBrowserTrack-69a92250cc8-Date-2024-03-20_Time-18-16-53.838136.log
In [40]:
options(repr.plot.width=15, repr.plot.height=6)
grid::grid.draw(p$Drd1)
In [41]:
grid::grid.draw(p$Drd2)
In [42]:
grid::grid.draw(p$Drd3)
In [43]:
grid::grid.draw(p$Foxp2)
In [44]:
grid::grid.draw(p$Tshz1)
In [ ]: