Figure 3
Florian Wuennemann
2024-03-08
Last updated: 2025-01-20
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Knit directory: mi_spatialomics/
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| File | Version | Author | Date | Message |
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| Rmd | 5e3046c | FloWuenne | 2024-12-15 | Updated Figure 3 and Supp Figure 7 with new region quantifications. |
| Rmd | 6478404 | FloWuenne | 2024-12-03 | Updated Supp Figure 5 and added celltype analysis markdown R1-1 and Figure 3 R2-4. |
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| Rmd | 56559c7 | FloWuenne | 2024-03-21 | Cleaned up repository. |
| Rmd | 21b927e | FloWuenne | 2024-03-17 | Updates supplementary figure code. |
Introduction
library(tidyverse)── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.1 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(data.table)Warning: package 'data.table' was built under R version 4.3.3
Attaching package: 'data.table'
The following objects are masked from 'package:lubridate':
hour, isoweek, mday, minute, month, quarter, second, wday, week,
yday, year
The following objects are masked from 'package:dplyr':
between, first, last
The following object is masked from 'package:purrr':
transposelibrary(ggbeeswarm)
source("./code/functions.R")
Attaching package: 'cowplot'
The following object is masked from 'package:lubridate':
stampWarning: package 'ggsci' was built under R version 4.3.3here() starts at /Users/florian_wuennemann/1_Projects/MI_project/1_Manuscript/Review_NCVR/mi_spatialomics## Read in quantified data
all_cell_types_quantified <- fread("./review/all_cell_types_per_region_counts_perctentages_20241212.csv")
ccr2_monomacro <- all_cell_types_quantified %>%
subset(final_cell_type == "Mono / Macros Ccr2+") %>%
subset(timepoint %in% c("4h","24h","48h")) %>%
subset(region_name %in% c("border_zone","infarct_core","epicardial_region","endocardial_region"))
ccr2_monomacro$region_name <- gsub("border_zone","Border zone",ccr2_monomacro$region_name)
ccr2_monomacro$region_name <- gsub("infarct_core","Infarct core",ccr2_monomacro$region_name)
ccr2_monomacro$region_name <- gsub("epicardial_region","Epicardium",ccr2_monomacro$region_name)
ccr2_monomacro$region_name <- gsub("endocardial_region","Endocardium",ccr2_monomacro$region_name)
ccr2_monomacro$region_name <- factor(ccr2_monomacro$region_name,
levels = c("Endocardium","Infarct core","Epicardium","Border zone"))
ccr2_monomacro$timepoint <- factor(ccr2_monomacro$timepoint,
levels = c("4h","24h","48h"))
seqIF_ccr2_relquant <- ggplot(ccr2_monomacro,aes(x = timepoint,y = count_per_mm2)) +
stat_summary(
fun.y = mean,
geom = "bar",
width = 0.9,
size = 0.3,
color = "black",
fill = "lightgrey") +
geom_beeswarm(size = 2, pch = 21, color = "black", aes(fill = region_name)) +
labs(x = "Time",
y = expression("Cells /"~mm^2)) +
#expression(paste("Mo / M",phi," per "~mm^2))
facet_grid(. ~ region_name) +
scale_fill_manual(values = c("#337272","#f0f0f0","#b062c2","#2c95c5")) +
theme(axis.title = element_text(face="bold"),
legend.position = "none") +
theme(panel.border = element_rect(color = "black", fill = NA, size = 0.75)) +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
axis.title.x = element_blank()) Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
ℹ Please use the `fun` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.seqIF_ccr2_relquant
save_plot(filename = "./plots/Figure_3.SeqIF-absolute_cell_counts.pdf",
plot = seqIF_ccr2_relquant,
base_asp = 1.8,
base_height = 3)
<br>
<p>
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<span class="glyphicon glyphicon-wrench" aria-hidden="true"></span>
Session information
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<div id="workflowr-sessioninfo" class="collapse">
``` r
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Toronto
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] RColorBrewer_1.1-3 here_1.0.1 ggsci_3.2.0 cowplot_1.1.3
[5] ggbeeswarm_0.7.2 data.table_1.16.2 lubridate_1.9.3 forcats_1.0.0
[9] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[13] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[17] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 beeswarm_0.4.0 xfun_0.49
[4] bslib_0.8.0 processx_3.8.4 callr_3.7.6
[7] tzdb_0.4.0 vctrs_0.6.5 tools_4.3.1
[10] ps_1.8.1 generics_0.1.3 fansi_1.0.6
[13] pkgconfig_2.0.3 lifecycle_1.0.4 farver_2.1.2
[16] compiler_4.3.1 git2r_0.35.0 textshaping_0.4.0
[19] munsell_0.5.1 getPass_0.2-4 vipor_0.4.7
[22] httpuv_1.6.15 htmltools_0.5.8.1 sass_0.4.9
[25] yaml_2.3.10 crayon_1.5.3 later_1.4.1
[28] pillar_1.9.0 jquerylib_0.1.4 whisker_0.4.1
[31] cachem_1.1.0 tidyselect_1.2.1 digest_0.6.37
[34] stringi_1.8.4 labeling_0.4.3 rprojroot_2.0.4
[37] fastmap_1.2.0 grid_4.3.1 colorspace_2.1-1
[40] cli_3.6.3 magrittr_2.0.3 utf8_1.2.4
[43] withr_3.0.2 scales_1.3.0 promises_1.3.2
[46] timechange_0.3.0 rmarkdown_2.29 httr_1.4.7
[49] ragg_1.3.3 hms_1.1.3 evaluate_1.0.1
[52] knitr_1.49 rlang_1.1.4 Rcpp_1.0.13-1
[55] glue_1.8.0 BiocManager_1.30.25 renv_1.0.3
[58] rstudioapi_0.17.1 jsonlite_1.8.9 R6_2.5.1
[61] systemfonts_1.1.0 fs_1.6.5