GitHub - lat exerscinse update

.gitignore

@@ -5,3 +5,4 @@ venv
 .DS_Store
 .Rhistory
 .Rdata
+*.html

Class_10/Class_10.Rmd

@@ -2,18 +2,13 @@
 title: "Class 10"
 author: "Szymon Drobniak"
 date: "`r Sys.Date()`"
-output:
-  md_document:
-    toc: true
-    variant: markdown_github
+output: rmdformats::robobook
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = FALSE)
+knitr::opts_chunk$set(echo = F)
 ```
 
-# Class 10
-
 **In the below instructions...**
 
 **EXERCISE 1:** are bits of code to execute/practice pieces to do, often with only hints on how to perform them.
@@ -329,7 +324,7 @@ Control over the graphical parameters in the `plot()` function is rudimentary. T
 A simple *ggplot2* graph may be structured as follows:
 
 ```{r eval = FALSE, include = T, echo = T}
-mygraph <- ggplot2(data = MYDATA,
+mygraph <- ggplot(data = MYDATA,
                   mapping = aes(x = VAR1, y = VAR2, ...)) +
   geom_1(OPTIONS) +
   geom_2(OPTIONS)
@@ -342,7 +337,7 @@ plot(graph2)
 
 Calling the `ggplot()` function may be used only to create an object of class `ggplot`, without displaying the actual graph. Such object will contain the data and its mappings to specific elements of the final plot. To display it, we need additional function from the `geom_...` family, which add specific visual elements to the defined mappings (e.g. `geom_point` adds scatterpoints, `geom_hist` forms a histogram). Subsequent elements can be concatenated using the `+` operator. other elements that can be added to the plot using `+` are display and aesthetic rules, e.g. `theme()`, which describe the appearance of non-data elements of a plot.
 
-Load the `ggplot2` - if you don;t have it use `install.packages()` to install it.
+Load the `ggplot2` - if you don't have it use `install.packages()` to install it.
 
 ```{r echo = T}
 # install.packages('ggplot2')

Class_12/Class_12.Rmd

@@ -2,18 +2,13 @@
 title: "Class 12"
 author: "Szymon Drobniak"
 date: "`r Sys.Date()`"
-output:
-  md_document:
-    toc: true
-    variant: markdown_github
+output: rmdformats::robobook
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = FALSE)
+knitr::opts_chunk$set(echo = F)
 ```
 
-# Class 12
-
 **In the below instructions...**
 
 **EXERCISE 1:** are bits of code to execute/practice pieces to do, often with only hints on how to perform them.
@@ -393,6 +388,83 @@ myplot <- ggplot(data = mydata, mapping = aes(x = Height, y = weight6weeks, colo
 myplot
 ```
 
+## Other geometries
+
+### Barplot
+
+```{r echo = T}
+myplot <- ggplot(data = mydata, mapping = aes(x = as.factor(Diet),
+                                            fill = as.factor(gender),
+                                            y = ..count..)) +
+  geom_bar() + 
+  labs(x = "Diet type", y = "Count", fill = "Diet") +
+  scale_x_discrete(labels = c('vegan','lacto-ovo', 'vegeterian')) +
+  scale_fill_discrete(labels = c('f', 'm')) +
+  theme_classic() +
+  theme(text = element_text(size = 20))
+
+# ggplot2 automatically counts things (..count.. is optional)
+
+myplot
+
+myplot <- ggplot(data = mydata, mapping = aes(x = as.factor(Diet),
+                                            fill = as.factor(gender),
+                                            y = ..count..)) +
+  geom_bar(position = "dodge") + 
+  labs(x = "Diet type", y = "Count", fill = "Diet") +
+  scale_x_discrete(labels = c('vegan','lacto-ovo', 'vegeterian')) +
+  scale_fill_discrete(labels = c('f', 'm')) +
+  theme_classic() +
+  theme(text = element_text(size = 20))
+
+# ggplot2 automatically counts things (..count.. is optional)
+
+myplot
+```
+
+
+### Error bars
+
+```{r echo =T}
+library(tidyverse)
+
+summ <- tibble(Age = levels(data_chol$AgeGroup),
+               mean = by(data_chol$After8weeks, data_chol$AgeGroup, mean, na.rm = T),
+               se = by(data_chol$After8weeks, data_chol$AgeGroup,
+                       function(x) sd(x, na.rm = T)/sqrt(length(x))))
+
+myplot <- ggplot(data = summ, mapping = aes(x = Age, y = mean,
+                                            ymin = mean-se, ymax = mean+se)) +
+  geom_bar(stat = 'identity', fill = 'white', colour = 'black') +
+  geom_errorbar(width = 0.5) +
+  theme_classic() +
+  theme(text = element_text(size = 20)) +
+  labs(y = "Cholesterol conc. after 8 weeks") +
+  scale_x_discrete(limits = c('Young', 'Middle', 'Old'))
+myplot
+
+myplot <- ggplot(data = summ, mapping = aes(x = Age, y = mean,
+                                            ymin = mean-se, ymax = mean+se)) +
+  geom_point(colour = 'black', cex = 5) +
+  geom_errorbar(width = 0.5) +
+  theme_classic() +
+  theme(text = element_text(size = 20)) +
+  labs(y = "Cholesterol conc. after 8 weeks") +
+  scale_x_discrete(limits = c('Young', 'Middle', 'Old'))
+myplot
+
+myplot <- ggplot(data = summ, mapping = aes(x = Age, y = mean,
+                                            ymin = mean-se, ymax = mean+se)) +
+  geom_point(colour = 'black', cex = 5) +
+  geom_errorbar(width = 0.5) +
+  theme_classic() +
+  theme(text = element_text(size = 20)) +
+  labs(y = "Cholesterol conc. after 8 weeks") +
+  scale_x_discrete(limits = c('Young', 'Middle', 'Old')) +
+  ylim(c(0, 6.5))
+myplot
+```
+
 
 ## Saving the plots