library(tidyverse)
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.2
## ✔ ggplot2 3.5.2 ✔ tibble 3.3.0
## ✔ lubridate 1.9.4 ✔ tidyr 1.3.1
## ✔ purrr 1.1.0
## ── 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 errors
library(dplyr)
library(purrr)
library(stringr)
conditions <- read.csv("conditions_annotation.csv")
expression <- read.csv("SC_expression.csv")
mlabels <- read.csv("mergedLabels.csv")
ThirtySevenDegree <-conditions[grepl("37 deg",conditions$primary),]
myexpression2 <-
expression %>%
dplyr::select(ThirtySevenDegree$ID)
tidyExpression <- myexpression2 %>% pivot_longer(cols = everything())
by_treatment <- tidyExpression %>%
group_by(name)
by_treatment %>%
summarise_all(list(mean = mean, median = median, n=length))
## # A tibble: 8 × 4
## name mean median n
## <chr> <dbl> <dbl> <int>
## 1 SAABFI 165. 20.3 6071
## 2 SAABFN 165. 17.7 6071
## 3 SAABFS 165. 17.3 6071
## 4 SAABIB 165. 16.6 6071
## 5 SAABIC 165. 15.9 6071
## 6 SAABIF 165. 20.0 6071
## 7 SAABIQ 165. 19.3 6071
## 8 SAABQR 165. 17.6 6071
ggplot(tidyExpression, aes(x=name,y=log(value), fill = name, color = name)) +
geom_violin() +
theme_classic()+
scale_color_brewer(palette="PuRd")+
scale_fill_brewer(palette = "BuPu")
## Warning: Removed 1407 rows containing non-finite outside the scale range
## (`stat_ydensity()`).
