Plotting Exercise 2

These exercises cover the sections on Plotting in R PlottingInR.

Section 1

• Please load the dateset SubsetRlog_7D.csv from "data/SubsetRlog_7D.csv"

• hint: use read.csv() function to load SubsetRlog_7D.csv. If you failed to import SubsetRlog_7D.csv to R, please check whether you set up your work directory properly by using getwd() and setwd()

##                    X  DOX24H_1  DOX24H_2  DOX24H_3   DOX7D_1   DOX7D_2
## 1 ENSMUSG00000050711 12.109594 12.155740 12.089761 13.891323 13.856755
## 2 ENSMUSG00000026463 12.288243 12.069297 11.934777 11.971843 11.908514
## 3 ENSMUSG00000051079  7.177476  7.282678  7.415341  8.097972  8.558204
## 4 ENSMUSG00000037995  9.178713  9.370469  9.047744  7.834046  7.667787
## 5 ENSMUSG00000039910  9.024315  8.790573  8.878026  9.497840  9.751352
## 6 ENSMUSG00000019880  8.308681  8.701553  8.403844  9.026944  9.351475
##     DOX7D_3  VEH24H_1  VEH24H_2  VEH24H_3   VEH7D_1   VEH7D_2   VEH7D_3
## 1 14.095029 12.361107 12.560950 12.404746 13.640879 13.552177 13.578203
## 2 11.748345 12.543844 12.334998 12.195093 12.357483 12.181816 12.315383
## 3  8.653715  6.761927  6.861818  6.899967  7.445987  7.440482  7.938914
## 4  7.540055  9.222387  9.152175  9.299462  8.064490  7.994608  8.025586
## 5  9.731984  9.257527  9.246675  9.442477  9.346837  9.238912  9.323775
## 6  9.373127  8.305506  8.296453  8.429132  8.762056  8.791535  8.877247

1. transform the wide data.frame to the long data.frame using melt() function from reshape2 package

2. add columns 'Treatment', 'TimePoint' and "Rep" based on 'variable' column information

• hint: check how to use sub() function by using ?sub

3. add columns 'Group' based on 'Treatment' and 'TimePoint' columns

• hint: check how to use paste() function by using ?paste

4. Please create the figure below using geom_boxplot() + geom_point()

• hint: The x-axis labels can be rotated 45 degrees by using theme(axis.text.x = element_text(angle=45, hjust=1))

## Warning in register(): Can't find generic `scale_type` in package ggplot2 to
## register S3 method.

5. Please create the figure below using geom_violin() + geom_boxplot()

• hint: please see the difference between geom_boxplot() and geom_boxplot(position = position_dodge(0.9),width=0.4)