figures.supplementary_figure_5
FloWuenne
2023-06-12
Last updated: 2024-03-21
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Knit directory: mi_spatialomics/
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| Rmd | b760056 | FloWuenne | 2024-01-31 | Updated Supplementary Figure 4. |
Introduction
# Load data
qc_dir <- "../data/nf-core_molkart/molkartqc"
files <- fs::dir_ls(path = qc_dir, glob = "*csv")
qc_data <- vroom(files)Rows: 48 Columns: 12
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): sample_id, segmentation_method
dbl (10): total_cells, avg_area, total_spots, spot_assign_per_cell, spot_ass...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.qc_data <- qc_data %>%
separate(sample_id,
into = c("string","time","replicate","slide","segmentation"),
remove = TRUE) %>%
mutate("sample_ID" = paste(string,time,replicate,slide,sep= "_"))
qc_data$avg_area <- qc_data$avg_area *0.138 * 0.138
qc_data$time <- factor(qc_data$time,
levels = c("control","4h","2d","4d"))
qc_data$segmentation_method <- factor(qc_data$segmentation_method,
levels = c("mesmer","ilastik","cellpose"
))
final_samples <- c("sample_control_r1_s1","sample_control_r2_s1",
"sample_4h_r1_s1","sample_4h_r2_s2",
"sample_2d_r1_s1","sample_2d_r2_s1",
"sample_4d_r1_s2","sample_4d_r2_s1")
qc_data <- subset(qc_data,sample_ID %in% final_samples)
qc_data <- qc_data %>%
pivot_longer(total_cells:spot_assign_percent,
names_to = "group",
values_to = "values") %>%
subset(group %in% c("avg_area","spot_assign_per_cell","spot_assign_percent","total_cells"))Plot the data
qc_data$group <- gsub("avg_area",paste("Average area (","\U00B5","m2)",sep=""),qc_data$group)
qc_data$group <- gsub("spot_assign_per_cell","Spots / cell",qc_data$group)
qc_data$group <- gsub("spot_assign_percent","% spots in cells",qc_data$group)
qc_data$group <- gsub("total_cells","Total # cells ",qc_data$group)
spots_assigned <- ggplot(qc_data,aes(segmentation_method, y= values, group = segmentation_method)) +
geom_boxplot(aes(color = segmentation_method, fill = segmentation_method),
outlier.size = 0, alpha = 0.3) +
# coord_flip() +
scale_fill_brewer(palette = "Dark2") +
scale_color_brewer(palette = "Dark2") +
scale_x_discrete(labels=c("cellpose" = "Cellpose 2",
"ilastik" = "Ilastik Multicut",
"mesmer" = "Mesmer")) +
labs(x = "") +
theme(legend.position = "none") +
facet_wrap(~ group, scales = "free") +
theme(plot.background = element_rect(fill = "white")) +
geom_point(size = 3.5, aes(fill = segmentation_method), color = "black" ,
pch = 21, alpha = 1) +
panel_border()
spots_assigned
save_plot(filename = here("./plots/Supplementary_figure_3.segmentation_metrics.png"),
plot = spots_assigned,
base_height = 2.5,
base_width = 5)
save_plot(filename = here("./plots/Supplementary_figure_3.segmentation_metrics.pdf"),
plot = spots_assigned,
base_height = 6)
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: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] RColorBrewer_1.1-3 ggsci_3.0.0 ggbeeswarm_0.7.2 here_1.0.1
[5] cowplot_1.1.2 ggpubr_0.6.0 lubridate_1.9.3 forcats_1.0.0
[9] stringr_1.5.1 purrr_1.0.2 readr_2.1.5 tidyr_1.3.0
[13] ggplot2_3.4.4 tidyverse_2.0.0 tibble_3.2.1 dplyr_1.1.4
[17] vroom_1.6.5 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] beeswarm_0.4.0 gtable_0.3.4 xfun_0.41
[4] bslib_0.6.1 processx_3.8.3 rstatix_0.7.2
[7] callr_3.7.3 tzdb_0.4.0 vctrs_0.6.5
[10] tools_4.3.1 ps_1.7.6 generics_0.1.3
[13] parallel_4.3.1 fansi_1.0.6 highr_0.10
[16] pkgconfig_2.0.3 lifecycle_1.0.4 farver_2.1.1
[19] compiler_4.3.1 git2r_0.33.0 textshaping_0.3.7
[22] munsell_0.5.0 getPass_0.2-4 carData_3.0-5
[25] vipor_0.4.7 httpuv_1.6.14 htmltools_0.5.7
[28] sass_0.4.8 yaml_2.3.8 car_3.1-2
[31] later_1.3.2 pillar_1.9.0 crayon_1.5.2
[34] jquerylib_0.1.4 whisker_0.4.1 cachem_1.0.8
[37] abind_1.4-5 tidyselect_1.2.0 digest_0.6.34
[40] stringi_1.8.3 labeling_0.4.3 rprojroot_2.0.4
[43] fastmap_1.1.1 grid_4.3.1 colorspace_2.1-0
[46] cli_3.6.2 magrittr_2.0.3 utf8_1.2.4
[49] broom_1.0.5 withr_2.5.2 backports_1.4.1
[52] scales_1.3.0 promises_1.2.1 bit64_4.0.5
[55] timechange_0.2.0 rmarkdown_2.25 httr_1.4.7
[58] bit_4.0.5 ggsignif_0.6.4 ragg_1.2.7
[61] hms_1.1.3 evaluate_0.23 knitr_1.45
[64] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0
[67] BiocManager_1.30.22 renv_1.0.3 rstudioapi_0.15.0
[70] jsonlite_1.8.8 R6_2.5.1 systemfonts_1.0.5
[73] fs_1.6.3