---
title: "Casq2 Weight Project"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
    source_code: embed
    
---

```{r setup, include=FALSE}

library(tidyverse)
library(readxl)
library(ggplot2)
library(plotly)
library(tableone)
knitr::opts_chunk$set(message = FALSE)

```

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### A look at the data

```{r raw data}

casq2_weight <- read_excel("DVR Mice Dissections.xlsx", 
                               sheet = "R")


#AD Look at tableone::createTableOne for some better options than `summary`

vars <- c("sex", "body_weight", "body_length", "heart_weight", "tibia_average", "HT_Body_Wt", "HT_Body_Length", "HT_Tibia")
tableOne <- CreateTableOne(vars = vars, strata = c("genotype"), data = casq2_weight)
tableOne


vars2 <- c("genotype", "body_weight", "body_length", "heart_weight", "tibia_average", "HT_Body_Wt", "HT_Body_Length", "HT_Tibia")
table2 <- CreateTableOne(vars = vars2, strata = c("sex"), data = casq2_weight)
table2
```

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### Normality Tests

***
Heart Weight
```{r embryo}

shapiro.test(casq2_weight$heart_weight)



```

***
Body Weight
```{r Placenta}
shapiro.test(casq2_weight$body_weight)

```

***
Tibia Length Average
```{r EP}
shapiro.test(casq2_weight$tibia_average)

```

***

All variables passed normality test by being non-significant


### T-test

*** 
Heart Weight between Genotype T-Test
```{r ttest}

t.test(heart_weight ~ genotype, data = casq2_weight)


```



Visualizations {data-orientation=columns data-icon="fa-chart-bar"}
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### Heart Weight

```{r interactive}

jn_theme <- function(){
  theme_bw() +
    theme(axis.text = element_text(size = 14, color = "Black"),
          axis.title = element_text(size = 16),
          panel.grid.minor = element_blank(),
          strip.text = element_text(size=14),
          strip.background = element_blank(),
          plot.title = element_text(size = 20, hjust = 0.5),
          panel.grid.major.x = element_blank())
}

heart_weight_viz <- ggplot(casq2_weight, aes(x=genotype, y=heart_weight)) + 
  geom_violin() + 
  theme_bw() + 
  geom_point(size = .5, height = 0, width = 0.05) + 
  scale_x_discrete(limits = c("WT", "Delta")) +
  stat_summary(fun.y = mean, geom="point", shape = 18, size  = 3, color = "red") + 
  stat_summary(fun.y = median,  geom = "point", shape = 3, size = 3, color = "blue")

heart_weight_viz

library(plotly)

ggplotly(heart_weight_viz, tooltip = c("heart_weight", "sex"))%>%layout(violinmode = 'group', violingap = 1, violingroupgap = 1)

```


### Heart Weight Normalized to Body Weight

```{r interactive2}

jn_theme <- function(){
  theme_bw() +
    theme(axis.text = element_text(size = 14, color = "Black"),
          axis.title = element_text(size = 16),
          panel.grid.minor = element_blank(),
          strip.text = element_text(size=14),
          strip.background = element_blank(),
          plot.title = element_text(size = 20, hjust = 0.5),
          panel.grid.major.x = element_blank())
}

heart_weight_body_weight <- ggplot(casq2_weight, aes(x=genotype, y=HT_Body_Wt)) + 
  geom_violin() + 
  theme_bw() + 
  geom_point(size = .5, height = 0, width = 0.05) + 
  scale_x_discrete(limits = c("WT", "Delta")) +
  stat_summary(fun.y = mean, geom="point", shape = 18, size  = 3, color = "red") + 
  stat_summary(fun.y = median,  geom = "point", shape = 3, size = 3, color = "blue")

heart_weight_body_weight

library(plotly)

ggplotly(heart_weight_body_weight, tooltip = c("HT_Body_Wt", "sex"))%>%layout(violinmode = 'group', violingap = 1, violingroupgap = 1)

```


### Heart Weight Normalized to Tibia Length

```{r interactive3}

jn_theme <- function(){
  theme_bw() +
    theme(axis.text = element_text(size = 14, color = "Black"),
          axis.title = element_text(size = 16),
          panel.grid.minor = element_blank(),
          strip.text = element_text(size=14),
          strip.background = element_blank(),
          plot.title = element_text(size = 20, hjust = 0.5),
          panel.grid.major.x = element_blank())
}

heart_weight_tibia_length <- ggplot(casq2_weight, aes(x=genotype, y=HT_Tibia)) + 
  geom_violin() + 
  theme_bw() + 
  geom_point(size = .5, height = 0, width = 0.05) + 
  scale_x_discrete(limits = c("WT", "Delta")) +
  stat_summary(fun.y = mean, geom="point", shape = 18, size  = 3, color = "red") + 
  stat_summary(fun.y = median,  geom = "point", shape = 3, size = 3, color = "blue")

heart_weight_tibia_length

library(plotly)

ggplotly(heart_weight_tibia_length, tooltip = c("HT_Tibia", "sex"))%>%layout(violinmode = 'group', violingap = 1, violingroupgap = 1)

```


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Dashboard made by Jacob Noeker