diff --git a/code/analysis/14_spatial_registration_PEC/00_data_check.R b/code/analysis/14_spatial_registration_PEC/00_data_check.R index 0c7d3d00..ecee993a 100644 --- a/code/analysis/14_spatial_registration_PEC/00_data_check.R +++ b/code/analysis/14_spatial_registration_PEC/00_data_check.R @@ -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", @@ -24,6 +24,7 @@ pec_cell_types <- c( "Oligo", "PC", "SMC", + "VLMC", # Excit (9) "L2/3 IT", "L4 IT", @@ -34,7 +35,7 @@ pec_cell_types <- c( "L6 IT", "L6 IT Car3", "L6b", - # Inhib (10) + # Inhib (9) "Chandelier", "Lamp5", "Lamp5 Lhx6", @@ -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")) diff --git a/code/analysis/14_spatial_registration_PEC/logs/03_PEC_correlation_annotation.txt b/code/analysis/14_spatial_registration_PEC/logs/03_PEC_correlation_annotation.txt index a893a416..def5da27 100644 --- a/code/analysis/14_spatial_registration_PEC/logs/03_PEC_correlation_annotation.txt +++ b/code/analysis/14_spatial_registration_PEC/logs/03_PEC_correlation_annotation.txt @@ -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 @@ -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 @@ -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: @@ -273,12 +273,12 @@ 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 @@ -286,7 +286,7 @@ Saving 13 x 7 in image 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 ─────────────────────────────────────────────────────────────────────────────────────────────────────────── @@ -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) @@ -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 diff --git a/code/analysis/14_spatial_registration_PEC/logs/07_PEC_annotation_Dx_plots.txt b/code/analysis/14_spatial_registration_PEC/logs/07_PEC_annotation_Dx_plots.txt index da92386f..c689a6e4 100644 --- a/code/analysis/14_spatial_registration_PEC/logs/07_PEC_annotation_Dx_plots.txt +++ b/code/analysis/14_spatial_registration_PEC/logs/07_PEC_annotation_Dx_plots.txt @@ -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 @@ -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) @@ -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 diff --git a/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.pdf b/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.pdf index 62348d6a..22d7a707 100644 Binary files a/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.pdf and b/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.pdf differ diff --git a/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.png b/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.png index 23da8501..7db87760 100644 Binary files a/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.png and b/plots/14_spatial_registration_PEC/03_PEC_correlation_annotation/registration_anno_dotplot_all.png differ diff --git a/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.pdf b/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.pdf index ce54a4c1..6fb8be2f 100644 Binary files a/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.pdf and b/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.pdf differ diff --git a/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.png b/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.png index 0256f4f4..1345d9e4 100644 Binary files a/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.png and b/plots/14_spatial_registration_PEC/07_PEC_annotation_Dx_plot/registration_anno_dotplot_control.png differ