Benjamin Ostendorf 2022-08-08
library(patchwork)
library(ggpubr)
library(RColorBrewer)
library(tidyverse)
source("../auxiliary/helper_functions.R")
knitr::opts_chunk$set(fig.retina = 3)## Import data
df_lungs <- read_tsv("../data/FC_lungs.tsv")##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## CD11b = col_double(),
## Ly6C = col_double(),
## Ly6G = col_double(),
## CD4 = col_double(),
## CD8 = col_double(),
## B_cells = col_double(),
## NK_cells = col_double(),
## Genotype = col_character()
## )
## Select variables
pops_to_plot <- colnames(df_lungs)[1:7]
## Plot
for (v in pops_to_plot) {
label.y_coordinates <- c(rep(max(as.numeric(df_lungs[[v]])) * 1.05, 2),
max(as.numeric(df_lungs[[v]])) * 1.2)
alternative_t_test <- if (v %in% c("CD11b", "Ly6C", "Ly6G")) "greater" else "less"
p_variable <-
df_lungs |>
ggplot(aes_string(x = "Genotype", fill = "Genotype", y = v)) +
geom_boxplot(outlier.shape = NA) +
ggbeeswarm::geom_quasirandom(size = 0.75, alpha = 0.6, shape = 21,
color = "white", fill = "black", stroke = 0.2) +
stat_compare_means(method = "t.test", method.args = list(alternative = alternative_t_test),
comparisons = APOE_contrasts_small,
label = "p.format", size = 1.75, label.y = label.y_coordinates) +
scale_fill_manual(values = pal_APOE) +
guides(x = guide_axis(angle = 60)) +
expand_limits(y = c(0, max(as.numeric(df_lungs[[v]])) * 1.3)) +
labs(title = gsub("_", " ", v),
y = bquote('Fraction of '~CD45^{textstyle("+")}),
x = "Genotype") +
theme_custom2 +
theme(legend.position = "none",
title = element_text(size = 7),
axis.text.x = element_text(face = "italic")) +
lemon::coord_capped_cart(left = "both", bottom = "both")
print(p_variable)
}
df_tetramer <- read_tsv("../data/FC_tetramer.tsv")##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## genotype = col_character(),
## tetramer = col_double()
## )
df_tetramer |>
ggplot(aes(x = genotype, fill = genotype, y = tetramer)) +
geom_boxplot(outlier.shape = NA) +
ggbeeswarm::geom_quasirandom(size = 0.75, alpha = 0.6, shape = 21,
color = "white", fill = "black", stroke = 0.2) +
stat_compare_means(method = "t.test", method.args = list(var.equal = FALSE),
comparisons = APOE_contrasts,
label = "p.format", size = 1.75, label.y = c(20, 20, 22)) +
scale_fill_manual(values = pal_APOE) +
guides(x = guide_axis(angle = 60)) +
expand_limits(y = c(0, max(as.numeric(df_tetramer$tetramer)) * 1.4)) +
labs(title = "Tetramer+", y = "Fraction of CD8+ (%)", x = "Genotype") +
theme_custom2 +
theme(legend.position = "none",
title = element_text(size = 7),
axis.text.x = element_text(face = "italic")) +
lemon::coord_capped_cart(left = "both", bottom = "both")
## ---------------------------------------------
## Import data
## ---------------------------------------------
df_PB_abs <- read_tsv("../data/FC_PB_abs.tsv")##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## genotype = col_character(),
## CD45 = col_double()
## )
df_PB <- read_tsv("../data/FC_PB.tsv")##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## genotype = col_character(),
## CD11b = col_double(),
## Ly6C = col_double(),
## Ly6G = col_double(),
## CD4 = col_double(),
## CD8 = col_double(),
## B_cells = col_double(),
## NK_cells = col_double()
## )
## ---------------------------------------------
## ED Fig 4d
## ---------------------------------------------
df_PB_abs |>
ggplot(aes(x = genotype, fill = genotype, y = CD45)) +
geom_boxplot(outlier.shape = NA) +
ggbeeswarm::geom_quasirandom(size = 0.75, alpha = 0.6, shape = 21,
color = "white", fill = "black", stroke = 0.2) +
stat_compare_means(method = "t.test", comparisons = APOE_contrasts,
label = "p.format", size = 1.75, label.y = c(3600, 3600, 4000)) +
scale_fill_manual(values = pal_APOE) +
guides(x = guide_axis(angle = 60)) +
expand_limits(y = c(0, 4000)) +
labs(title = "CD45+",
y = "Cells per µl",
x = "Genotype") +
theme_custom2 +
theme(legend.position = "none",
title = element_text(size = 7),
axis.text.x = element_text(face = "italic")) +
lemon::coord_capped_cart(left = "both", bottom = "both")
## ---------------------------------------------------------------
## ED Fig 4e-f
## ---------------------------------------------------------------
cell_populations <- colnames(df_PB)[2:8]
for (v in cell_populations) {
label.y_coordinates <- c(rep(max(as.numeric(df_PB[[v]])) * 1.05, 2),
max(as.numeric(df_PB[[v]])) * 1.15)
p_variable <-
df_PB |>
ggplot(aes_string(x = "genotype", fill = "genotype", y = v)) +
geom_boxplot(outlier.shape = NA) +
ggbeeswarm::geom_quasirandom(size = 0.75, alpha = 0.6, shape = 21,
color = "white", fill = "black", stroke = 0.2) +
stat_compare_means(method = "t.test", comparisons = APOE_contrasts,
label = "p.format", size = 1.75, label.y = label.y_coordinates) +
scale_fill_manual(values = pal_APOE) +
guides(x = guide_axis(angle = 60)) +
expand_limits(y = c(0)) +
labs(title = gsub("_", " ", v),
y = "Fraction of CD45+ (%)",
x = "Genotype") +
theme_custom2 +
theme(legend.position = "none",
title = element_text(size = 7),
axis.text.x = element_text(face = "italic")) +
lemon::coord_capped_cart(left = "both", bottom = "both")
print(p_variable)
}
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.0 (2021-05-18)
## os macOS Big Sur 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Berlin
## date 2022-08-24
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.0)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
## backports 1.2.1 2020-12-09 [1] CRAN (R 4.1.0)
## beeswarm 0.3.1 2021-03-07 [1] CRAN (R 4.1.0)
## broom 0.7.6 2021-04-05 [1] CRAN (R 4.1.0)
## cachem 1.0.5 2021-05-15 [1] CRAN (R 4.1.0)
## callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
## car 3.0-10 2020-09-29 [1] CRAN (R 4.1.0)
## carData 3.0-4 2020-05-22 [1] CRAN (R 4.1.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.0)
## cli 2.5.0 2021-04-26 [1] CRAN (R 4.1.0)
## colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.1.0)
## crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0)
## curl 4.3.1 2021-04-30 [1] CRAN (R 4.1.0)
## data.table 1.14.0 2021-02-21 [1] CRAN (R 4.1.0)
## DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0)
## dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.1.0)
## desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.0)
## devtools 2.4.1 2021-05-05 [1] CRAN (R 4.1.0)
## digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0)
## dplyr * 1.0.6 2021-05-05 [1] CRAN (R 4.1.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
## fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
## farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
## forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.1.0)
## foreign 0.8-81 2020-12-22 [1] CRAN (R 4.1.0)
## fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
## generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0)
## ggbeeswarm 0.6.0 2017-08-07 [1] CRAN (R 4.1.0)
## ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
## ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.1.0)
## ggsignif 0.6.1 2021-02-23 [1] CRAN (R 4.1.0)
## glue 1.6.0 2021-12-17 [1] CRAN (R 4.1.0)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
## haven 2.4.1 2021-04-23 [1] CRAN (R 4.1.0)
## highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
## hms 1.1.0 2021-05-17 [1] CRAN (R 4.1.0)
## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.0)
## httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
## jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0)
## knitr 1.37 2021-12-16 [1] CRAN (R 4.1.0)
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## pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0)
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## ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
## purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
## RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
## Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
## readr * 1.4.0 2020-10-05 [1] CRAN (R 4.1.0)
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##
## [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library