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figure4_visuals.qmd
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figure4_visuals.qmd
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---
title: "figure_4"
author: "vb"
format: html
editor: source
---
## nuclei vs estimated cell number
### functions and library
```{r}
#libraries
library(tidyverse)
```
### set parameters and input
```{r}
#summarized_thp1
#summarized_c2c12
#summarized_a172
#summarized_a172_13
#summarized_a549
#summarized_a549_13
```
### THP1
```{r}
#| fig-width: 12
#| fig-height: 12
rho_thp1 <- cor.test(x=summarized_thp1$nuclei,
y=summarized_thp1$n, method = 'spearman') %>%
pluck("estimate") %>% unname()
label_rho <- paste0("R = ", round(rho_thp1, 3), ", p < 0.001")
summarized_thp1 %>%
filter(!str_detect(file, "E9")) %>% #E9 image is blurry
ggplot(aes(x = nuclei, y = n))+
geom_point(size = 10, alpha = 0.8, color = "darkgreen")+
geom_abline(slope=1, intercept = 0, linetype = "dotted")+
annotate(geom = "text",
x = 100,
y = 5000,
label = label_rho,
size = 12,
hjust = 0)+
annotate(geom = "text",
x = 500,
y = 100,
label = "... = y ~ x",
size = 12,
hjust = 0,
)+
labs(subtitle = "THP1",
x = "Number of nuclei",
y = "Estimated number of cells")+
lims(x = c(0, 5200),
y = c(0, 5200))+
theme_BF_larger() +
theme(legend.position = "none")+
theme(aspect.ratio = 1)
```
#### THP1 relative difference (rebuttal)
```{r}
summarized_thp1 %>%
select(file, n, nuclei) %>%
#filter(n>300) %>%
mutate(rel_diff = abs((n - nuclei)/n*100)) %>%
summarize(mean = median(rel_diff))
ggplot(aes( x = n, y = rel_diff))+
geom_point()
```
### C2C12
```{r}
#| fig-width: 12
#| fig-height: 12
rho_c2c12 <- cor.test(x=summarized_c2c12$nuclei,
y=summarized_c2c12$n, method = 'spearman') %>%
pluck("estimate") %>% unname()
label_rho <- paste0("R = ", round(rho_c2c12, 3), ", p < 0.001")
summarized_c2c12 %>%
ggplot(aes(x = nuclei, y = n))+
geom_point(size = 10, alpha = 0.8, color = "darkgreen")+
geom_abline(slope=1, intercept = 0, linetype = "dotted")+
annotate(geom = "text",
x = 100,
y = 2000,
label = label_rho,
size = 12,
hjust = 0)+
annotate(geom = "text",
x = 200,
y = 100,
label = "... = y ~ x",
size = 12,
hjust = 0,
)+
labs(subtitle = "C2C12",
x = "Number of nuclei",
y = "Estimated number of cells")+
lims(x = c(0, 2100),
y = c(0, 2100))+
theme_BF_larger() +
theme(legend.position = "none")+
theme(aspect.ratio = 1)
```
#### C2C12 relative difference (rebuttal)
```{r}
summarized_c2c12 %>%
select(file, n, nuclei) %>%
#filter(n>300) %>%
mutate(rel_diff = log(n) - log(nuclei)) %>%
#summarize(mean = median(rel_diff))
ggplot(aes( x = nuclei, y = rel_diff))+
geom_point()
```
### A172
```{r}
#| fig-width: 12
#| fig-height: 12
my_rho <- cor.test(x=summarized_a172 %>%
filter(timepoint == 7) %>% pluck("nuclei"),
y=summarized_a172 %>% filter(timepoint == 7) %>% pluck("n"),
method = 'spearman') %>%
pluck("estimate") %>% unname()
label_rho <- paste0("R = ", round(my_rho, 3), ", p < 0.001")
summarized_a172 %>%
filter(timepoint == 7) %>%
ggplot(aes(x = nuclei, y = n))+
geom_point(size = 10, alpha = 0.8, color = "darkgreen")+
geom_abline(slope=1, intercept = 0, linetype = "dotted")+
annotate(geom = "text",
x = 20,
y = 1100,
label = label_rho,
size = 12,
hjust = 0)+
annotate(geom = "text",
x = 200,
y = 100,
label = "... = y ~ x",
size = 12,
hjust = 0,
)+
labs(subtitle = "A172 - 24h",
x = "Number of nuclei",
y = "Estimated number of cells")+
lims(x = c(0, 1100),
y = c(0, 1100))+
theme_BF_larger() +
theme(legend.position = "none")+
theme(aspect.ratio = 1)
my_rho <- cor.test(x=summarized_a172_13 %>%
filter(timepoint == 13) %>% pluck("nuclei"),
y=summarized_a172_13 %>% filter(timepoint == 13) %>% pluck("n"),
method = 'spearman') %>%
pluck("estimate") %>% unname()
label_rho <- paste0("R = ", round(my_rho, 3), ", p < 0.001")
summarized_a172_13 %>%
filter(timepoint == 13) %>%
ggplot(aes(x = nuclei, y = n))+
geom_point(size = 10, alpha = 0.8, color = "darkgreen")+
geom_abline(slope=1, intercept = 0, linetype = "dotted")+
annotate(geom = "text",
x = 20,
y = 2100,
label = label_rho,
size = 12,
hjust = 0)+
annotate(geom = "text",
x = 200,
y = 100,
label = "... = y ~ x",
size = 12,
hjust = 0,
)+
labs(subtitle = "A172 - 48h",
x = "Number of nuclei",
y = "Estimated number of cells")+
lims(x = c(0, 2200),
y = c(0, 2200))+
theme_BF_larger() +
theme(legend.position = "none")+
theme(aspect.ratio = 1)
```
### A549
```{r}
#| fig-width: 12
#| fig-height: 12
my_rho <- cor.test(x=summarized_a549 %>%
filter(timepoint == 7) %>% pluck("nuclei"),
y=summarized_a549 %>% filter(timepoint == 7) %>% pluck("n"),
method = 'spearman') %>%
pluck("estimate") %>% unname()
label_rho <- paste0("R = ", round(my_rho, 3), ", p < 0.001")
summarized_a549 %>%
filter(timepoint == 7) %>%
ggplot(aes(x = nuclei, y = n))+
geom_point(size = 10, alpha = 0.8, color = "darkgreen")+
geom_abline(slope=1, intercept = 0, linetype = "dotted")+
annotate(geom = "text",
x = 20,
y = 800,
label = label_rho,
size = 12,
hjust = 0)+
annotate(geom = "text",
x = 200,
y = 100,
label = "... = y ~ x",
size = 12,
hjust = 0,
)+
labs(subtitle = "A549 - 24h",
x = "Number of nuclei",
y = "Estimated number of cells")+
# lims(x = c(0, 2200),
# y = c(0, 2200))+
theme_BF_larger() +
theme(legend.position = "none")+
theme(aspect.ratio = 1)
my_rho <- cor.test(x=summarized_a549_13 %>%
filter(timepoint == 13) %>% pluck("nuclei"),
y=summarized_a549_13 %>% filter(timepoint == 13) %>% pluck("n"),
method = 'spearman') %>%
pluck("estimate") %>% unname()
label_rho <- paste0("R = ", round(my_rho, 3), ", p < 0.001")
summarized_a549_13 %>%
filter(timepoint == 13) %>%
ggplot(aes(x = nuclei, y = n))+
geom_point(size = 10, alpha = 0.8, color = "darkgreen")+
geom_abline(slope=1, intercept = 0, linetype = "dotted")+
annotate(geom = "text",
x = 20,
y = 2100,
label = label_rho,
size = 12,
hjust = 0)+
annotate(geom = "text",
x = 200,
y = 100,
label = "... = y ~ x",
size = 12,
hjust = 0,
)+
labs(subtitle = "A549 - 48h",
x = "Number of nuclei",
y = "Estimated number of cells")+
# lims(x = c(0, 2200),
# y = c(0, 2200))+
theme_BF_larger() +
theme(legend.position = "none")+
theme(aspect.ratio = 1)
```
#### my used function in this file
```{r}
#qmd code copied to R file
#NCmisc::list.functions.in.file(here::here("prepration.R"))
```
all functions and packages in this files:
\$.GlobalEnv \[1\] "theme_BF_larger"
\$`c("package:dplyr", "package:stats")` \[1\] "filter"
\$`package:base` \[1\] "c" "library" "paste0" "round" "unname"
\$`package:ggplot2` \[1\] "aes" "annotate" "geom_abline" "geom_point" "ggplot"\
\[6\] "labs" "lims" "theme"
\$`package:purrr` \[1\] "pluck"
\$`package:stats` \[1\] "cor.test"
\$`package:stringr` \[1\] "str_detect"