figures.supplementary_figure_5
FloWuenne
2023-06-12
Last updated: 2023-06-12
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Knit directory: mi_spatialomics/
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# Load data
qc_dir <- "/Users/florian_wuennemann/1_Projects/MI_project/data/nf_MolCart_results/QC"
files <- fs::dir_ls(path = qc_dir, glob = "*csv")
qc_data <- vroom(files)Rows: 64 Columns: 8
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): sample_id, segmentation_method
dbl (6): total_cells, avg_area, total_spots, spot_assign_per_cell, spot_assi...
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= "_"))Warning: Expected 5 pieces. Additional pieces discarded in 48 rows [2, 3, 4, 6, 7, 8,
10, 11, 12, 14, 15, 16, 18, 19, 20, 22, 23, 24, 26, 27, ...].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("ilastik_multicut","cellpose",
"mesmer_wholecell","mesmer_nuclear"
))
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"))
qc_data$group <- gsub("avg_area","Average area (uM^2)",qc_data$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,values)) +
geom_boxplot(aes(fill = segmentation_method)) +
coord_flip() +
scale_fill_brewer(palette = "Set1") +
scale_color_brewer(palette = "Set1") +
scale_x_discrete(labels=c("ilastik_multicut" = "Ilastik Multicut",
"cellpose" = "Cellpose",
"mesmer_wholecell" = "Mesmer - Whole cell",
"mesmer_nuclear" = "Mesmer - Nuclear")) +
labs(x = "",
y = "") +
theme(legend.position = "none") +
facet_grid(. ~ group, scales = "free") +
theme(plot.background = element_rect(fill = "white")) +
geom_beeswarm(fill = "white",color= "black",pch = 21) +
panel_border()
spots_assigned
save_plot(filename = here("./figures/Supplementary_figure_5.segmentation_metrics.png"),
plot = spots_assigned,
base_height = 6)
save_plot(filename = here("./figures/Supplementary_figure_5.segmentation_metrics.eps"),
plot = spots_assigned,
base_height = 5,
base_width = 10)
sessionInfo()R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] ggbeeswarm_0.7.2 here_1.0.1 cowplot_1.1.1 ggpubr_0.6.0
[5] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 purrr_1.0.1
[9] readr_2.1.4 tidyr_1.3.0 ggplot2_3.4.2 tidyverse_2.0.0
[13] tibble_3.2.1 dplyr_1.1.2 vroom_1.6.3 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] httr_1.4.6 sass_0.4.6 bit64_4.0.5 jsonlite_1.8.4
[5] carData_3.0-5 bslib_0.4.2 getPass_0.2-2 highr_0.10
[9] renv_0.17.3 vipor_0.4.5 yaml_2.3.7 pillar_1.9.0
[13] backports_1.4.1 glue_1.6.2 digest_0.6.31 RColorBrewer_1.1-3
[17] promises_1.2.0.1 ggsignif_0.6.4 colorspace_2.1-0 htmltools_0.5.5
[21] httpuv_1.6.11 pkgconfig_2.0.3 broom_1.0.5 scales_1.2.1
[25] processx_3.8.0 whisker_0.4.1 later_1.3.1 tzdb_0.4.0
[29] timechange_0.2.0 git2r_0.32.0 generics_0.1.3 farver_2.1.1
[33] car_3.1-2 cachem_1.0.8 withr_2.5.0 cli_3.6.1
[37] magrittr_2.0.3 crayon_1.5.2 evaluate_0.21 ps_1.7.4
[41] fs_1.6.2 fansi_1.0.4 rstatix_0.7.2 beeswarm_0.4.0
[45] textshaping_0.3.6 tools_4.2.3 hms_1.1.3 lifecycle_1.0.3
[49] munsell_0.5.0 callr_3.7.3 compiler_4.2.3 jquerylib_0.1.4
[53] systemfonts_1.0.4 rlang_1.1.1 grid_4.2.3 rstudioapi_0.14
[57] labeling_0.4.2 rmarkdown_2.21 gtable_0.3.3 abind_1.4-5
[61] R6_2.5.1 knitr_1.42 fastmap_1.1.1 bit_4.0.5
[65] utf8_1.2.3 rprojroot_2.0.3 ragg_1.2.5 stringi_1.7.12
[69] parallel_4.2.3 Rcpp_1.0.10 vctrs_0.6.2 tidyselect_1.2.0
[73] xfun_0.39