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Fix VLCM class
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@lahuuki
lahuuki committed Feb 7, 2023
1 parent d7d386b commit 6f90da3
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Showing 7 changed files with 31 additions and 31 deletions.
8 changes: 4 additions & 4 deletions code/analysis/14_spatial_registration_PEC/00_data_check.R
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ data_dir <-

#### Define PEC & store cell type details ####
pec_cell_types <- c(
# Non-neuronal cells (8)
# Non-neuronal cells (9)
"Astro",
"Endo",
"Immune",
Expand All @@ -24,6 +24,7 @@ pec_cell_types <- c(
"Oligo",
"PC",
"SMC",
"VLMC",
# Excit (9)
"L2/3 IT",
"L4 IT",
Expand All @@ -34,7 +35,7 @@ pec_cell_types <- c(
"L6 IT",
"L6 IT Car3",
"L6b",
# Inhib (10)
# Inhib (9)
"Chandelier",
"Lamp5",
"Lamp5 Lhx6",
Expand All @@ -43,14 +44,13 @@ pec_cell_types <- c(
"Sncg",
"Sst",
"Sst Chodl",
"VLMC",
"Vip"
)

pec_cell_type_tb <- tibble(
cell_type = factor(pec_cell_types, levels = pec_cell_types),
cluster = make.names(cell_type),
ct_cat = unlist(map2(c("Non-neuronal", "Excit", "Inhib"), c(8, 9, 10), rep))
ct_cat = unlist(map2(c("Non-neuronal", "Excit", "Inhib"), c(9, 9, 9), rep))
)

save(pec_cell_type_tb, file = here(data_dir, "pec_cell_type_tb.Rdata"))
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42 changes: 21 additions & 21 deletions code/analysis/14_spatial_registration_PEC/logs/03_PEC_correlation_annotation.txt
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Expand Up @@ -6,12 +6,12 @@ Loading LIBD module for rmate/1.5.9
Loading LIBD module for ruby/2.6.4p104
Loading conda_R/4.2.x
**** Job starts ****
Thu Feb 2 09:22:39 EST 2023
Mon Feb 6 19:04:56 EST 2023
**** JHPCE info ****
User: lhuuki
Job id: 2886093
Job id: 2904731
Job name: PEC_correlation_annotation
Hostname: compute-091.cm.cluster
Hostname: compute-115.cm.cluster
Task id: undefined
Unloading conda_R/4.2.x
Loading conda_R/4.2.x
Expand Down Expand Up @@ -139,18 +139,18 @@ This message can be suppressed by:

here() starts at /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC
snapshotDate(): 2022-10-31
2023-02-02 09:23:21 loading file /users/lhuuki/.cache/R/BiocFileCache/6b24121203e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
2023-02-06 19:05:38 loading file /users/lhuuki/.cache/R/BiocFileCache/6b24121203e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
[1] "layer" "k09" "k16"
Loading objects:
pec_cell_type_tb
2023-02-02 09:23:25 - CMC
2023-02-02 09:23:25 - DevBrain-snRNAseq
2023-02-02 09:23:26 - IsoHuB
2023-02-02 09:23:27 - LIBD
2023-02-02 09:23:28 - MultiomeBrain-DLPFC
2023-02-02 09:23:29 - PTSDBrainomics
2023-02-02 09:23:29 - SZBDMulti-Seq
2023-02-02 09:23:30 - UCLA-ASD
2023-02-06 19:05:41 - CMC
2023-02-06 19:05:41 - DevBrain-snRNAseq
2023-02-06 19:05:41 - IsoHuB
2023-02-06 19:05:42 - LIBD
2023-02-06 19:05:43 - MultiomeBrain-DLPFC
2023-02-06 19:05:44 - PTSDBrainomics
2023-02-06 19:05:44 - SZBDMulti-Seq
2023-02-06 19:05:44 - UCLA-ASD
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.poi.util.SAXHelper (file:/jhpce/shared/jhpce/core/conda/miniconda3-4.11.0/envs/svnR-4.2.x/R/4.2.x/lib64/R/site-library/xlsxjars/java/poi-ooxml-3.10.1-20140818.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int)
WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.SAXHelper
Expand Down Expand Up @@ -229,8 +229,8 @@ Joining with `by = join_by(Annotation, layers)`
6 CMC layer Oligo 1
7 CMC layer PC 1
8 CMC layer SMC 1
9 CMC layer L2/3 IT 1
10 CMC layer L4 IT 1
9 CMC layer VLMC 1
10 CMC layer L2/3 IT 1
# … with 145 more rows
Joining with `by = join_by(Domain, cellType)`
Warning message:
Expand Down Expand Up @@ -273,20 +273,20 @@ Warning messages:
Saving 13 x 7 in image
Saving 13 x 7 in image
[1] "Reproducibility information:"
[1] "2023-02-02 09:23:52 EST"
[1] "2023-02-06 19:06:05 EST"
user system elapsed
46.402 3.019 70.986
59.260 2.994 65.577
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.2 Patched (2023-02-01 r83749)
version R version 4.2.2 Patched (2023-02-05 r83768)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz US/Eastern
date 2023-02-02
date 2023-02-06
pandoc 2.19.2 @ /jhpce/shared/jhpce/core/conda/miniconda3-4.11.0/envs/svnR-4.2.x/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
Expand Down Expand Up @@ -355,14 +355,14 @@ Saving 13 x 7 in image
fs 1.6.0 2023-01-23 [2] CRAN (R 4.2.2)
gargle 1.3.0 2023-01-30 [2] CRAN (R 4.2.2)
generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.1)
GenomeInfoDb * 1.34.7 2023-01-24 [2] Bioconductor
GenomeInfoDb * 1.34.9 2023-02-02 [2] Bioconductor
GenomeInfoDbData 1.2.9 2022-09-29 [2] Bioconductor
GenomicAlignments 1.34.0 2022-11-01 [2] Bioconductor
GenomicRanges * 1.50.2 2022-12-16 [2] Bioconductor
GetoptLong 1.0.5 2020-12-15 [2] CRAN (R 4.2.1)
ggbeeswarm 0.7.1 2022-12-16 [2] CRAN (R 4.2.2)
ggplot2 * 3.4.0 2022-11-04 [2] CRAN (R 4.2.2)
ggrepel 0.9.2 2022-11-06 [2] CRAN (R 4.2.2)
ggrepel 0.9.3 2023-02-03 [2] CRAN (R 4.2.2)
GlobalOptions 0.1.2 2020-06-10 [2] CRAN (R 4.2.1)
glue 1.6.2 2022-02-24 [2] CRAN (R 4.2.1)
golem 0.3.5 2022-10-18 [2] CRAN (R 4.2.1)
Expand Down Expand Up @@ -494,4 +494,4 @@ Saving 13 x 7 in image

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
**** Job ends ****
Thu Feb 2 09:23:54 EST 2023
Mon Feb 6 19:06:10 EST 2023
12 changes: 6 additions & 6 deletions code/analysis/14_spatial_registration_PEC/logs/07_PEC_annotation_Dx_plots.txt
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Expand Up @@ -6,12 +6,12 @@ Loading LIBD module for rmate/1.5.9
Loading LIBD module for ruby/2.6.4p104
Loading conda_R/4.2.x
**** Job starts ****
Mon Feb 6 18:49:26 EST 2023
Mon Feb 6 19:04:56 EST 2023
**** JHPCE info ****
User: lhuuki
Job id: 2904716
Job id: 2904730
Job name: PEC_annotation_Dx_plots
Hostname: compute-076.cm.cluster
Hostname: compute-105.cm.cluster
Task id: undefined
Unloading conda_R/4.2.x
Loading conda_R/4.2.x
Expand Down Expand Up @@ -218,9 +218,9 @@ Warning messages:
Saving 13 x 7 in image
Saving 13 x 7 in image
[1] "Reproducibility information:"
[1] "2023-02-06 18:50:55 EST"
[1] "2023-02-06 19:05:41 EST"
user system elapsed
41.781 3.591 85.366
23.024 1.828 42.001
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.2 Patched (2023-02-05 r83768)
Expand Down Expand Up @@ -431,4 +431,4 @@ Saving 13 x 7 in image

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
**** Job ends ****
Mon Feb 6 18:51:05 EST 2023
Mon Feb 6 19:05:45 EST 2023
Binary file modified ..._spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.pdf
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