Li submission for Exercise 10

.Rhistory

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+ls
+pwd
+ls
+x <- 3
+print x <- 3
+setwd
+install.packages("swirl")
+library(swirl)
+1
+swirl (1)
+library("swirl")
+swirl()
+1
+swirl()
+numeric(0.5, 55, -10, 6)
+numeric("0.5, 55, -10, 6")
+numeric("0.5", "55", "-10", "6")
+num_vect <- numeric("0.5", "55", "-10", "6")
+num_vect <- numeric("0.5","55","-10","6")
+num_vect <- numeric(0.5, 55, -10, 6)
+num_vect <- c(0.5, 55, -10, 6)
+swirl()
+swirl()
+0
+tf <- num_vect < 1
+print(tf)
+tf
+num_vect >= 6
+my_char <- c("my", "name", "is")
+my_char <- c("My", "name", "is")
+my_char
+paste(my_char, collapse = " ")
+my_name <- c(my_char, "Lan")
+my_name
+paste(my_name, collapse = " ")
+paste("Hello", "world!", sep = " ")
+paste(num_vect(1:3), c("X", "Y", "Z"), sep = "")
+paste(num_vect(1L:3L), c("X", "Y", "Z"), sep = "")
+paste(num_vect(1L:3L), c("X", "Y", "Z"), sep = "")
+paste(num_vect(1L, 2L, 3L), c("X", "Y", "Z"), sep = "")
+paste(c(1L, 2L, 3L), c("X", "Y", "Z"), sep = "")
+paste(1:3, c("X", "Y", "Z"), sep = "")
+paste(LETTERS, 1:4, sep = "-")
+5+7
+x <- 5+7
+x
+y <- x-3
+y
+0
+exit
+exit()
+c(1.1, 9, 3.14)
+z <- c(1.1, 9, 3.14)
+?c()
+?c
+z
+c(z, 555)
+c(z, 555, z)
+z*2+100
+my_sqrt <- sqrt
+my_sqrt <- sqrt(z-1)
+my_sqrt
+my_div <- my_sqrt/z
+my_div <- z / my_sqrt
+my_div
+c(1,2,3,4 + 0, 10)
+(1, 2, 3, 4) + c(0, 10)
+c(1, 2, 3, 4) + c(0, 10)
+c(1, 2, 3, 4) + c(0, 10, 100)
+c(1, 2, 3, 4) + c(0, 10, 100)
+c(1, 2, 3, 4) + c(0, 10, 1000)
+z*2+1000
+my_char
+my_div
+sqirl
+sqwirl
+swirl()
+swirl
+swirl::main()
+swirl::main()
+swirl
+swirl::swirl()
+getwd()
+ls()
+x <- 9
+ls
+ls()
+dir()
+?list.files
+args(list.files)
+getwd
+old.dir <- getwd()
+testdir <- dir.create()
+testdir <- dir.create(getwd)
+testdir <- dir.create(getwd())
+dir.create("testdir")
+setwd
+setwd("testdir")
+file.create("mytest.R")
+dir()
+file.exists()
+file.exists("mytest.R")
+file.info("mytest.R")
+args(file.rename)
+file.rename("mytest.R", "mytest2.R")
+file.copy("mytest2.R", "mytest3.R")
+file.path("mytest3.R")
+file.path("mytest3.R", 'folder1', 'folder2')
+file.path("folder1", "folder2")
+?dir.create
+dir.create(file.path ("testdir2", "testdir3"), recursive = recursive = TRUE)
+dir.create(file.path ("testdir2", "testdir3"), recursive = TRUE)
+setwd
+setwd()
+setwd(old.dir)
+1:20
+pi:10
+15:1
+?`:`
+seq(1:20)
+seq(1,20)
+seq(1,20, by=0.5)
+seq(1,10, by=0.5)
+seq(0,10, by=0.5)
+my_seq <- seq(5, 10, length=30)
+length(my_seq)
+seq(1:length(my_seq))
+1:length(my_seq)
+seq(along.with = my_seq)
+seq_along(my_seq)
+rep(0, times = 40)
+rep(c(0, 1, 2), times = 10)
+rep(c(0, 1, 2), each = 10)
+#a scatter plot of those two variables (time and the amount of cumulative drug release)
+setwd("Desktop/Biocomp_tutorial12/")
+a = read.table("drug_release.txt", header = T, stringsAsFactors = F, sep = " ")
+a = read.table("drug_release.txt", header = T, stringsAsFactors = F, sep = "")
+a = read.table("drug_release.txt", header = T, sep = "")
+a <-  read.table("drug_release.txt", header = T)
+a <-  read.table("drug_release.txt", header = T, sep = "")
+a <-  read.table("drug_release.txt", header = T, sep = "", fill = T)
+a
+a
+a
+library(ggplot2)
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", fill = T)
+a
+library(ggplot2)
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", fill = T)
+a
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "")
+a
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+a
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)")
+library(ggplot2)
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)")
+library(ggplot2)
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_bw()
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_bw()+
+theme(axis.text.x = element_text(angle=0, vjust=0.6))
+setwd("Desktop/Biocomp_tutorial12/")
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic()
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+setwd("Desktop/Biocomp_tutorial12/")
+library(ggplot2)
+rm(list = ls())
+#1. a scatter plot of those two variables (time and the amount of cumulative drug release)
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+# 2-1 a barplot of the means of the four populations
+b <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+b
+# 2-1 a barplot of the means of the four populations
+b <-  read.table("data.txt", header = T, sep = "", stringsAsFactors = F)
+b
+head(b)
+b <-  read.table("data.txt", header = T, sep = ",", stringsAsFactors = F)
+head(b)
+b <-  read.table("data.txt", header = T, sep = ",", stringsAsFactors = F)
+head(b)
+ggplot(b, aes(x = region, y = observations)) +
+stat_summary(fun = mean, geom = "bar") +
+xlab("region") +
+ylab("population") +
+theme_classic()
+?geom_scatterplot
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm") +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(method="lm",se=FALSE) +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point() +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point(size = 2) +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point(size = 3) +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point(size = 3) +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)", font = 4) +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+geom_point(size = 3) +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)", font = 10) +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release), font = 12) +
+geom_point(size = 3) +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release, font = 12)) +
+geom_point(size = 3) +
+stat_smooth(se=FALSE) +
+xlab("Time (hour)") +
+ylab("cumulative drug release (ng)") +
+theme_classic() +
+theme(legend.title=element_blank())
+ggplot(b, aes(x = region, y = observations)) +
+geom_scatterplot()
+ggplot(b, aes(x = region, y = observations)) +
+geom_jitter()
+#2-2 a scatter plot of all of the observations
+ggplot(b, aes(x = region, y = observations)) +
+geom_jitter(size = 1)
+ggplot(b, aes(x = region, y = observations)) +
+geom_jitter(size = 1)+
+theme_classic()
+b <-  read.table("data.txt", header = T, sep = ",", stringsAsFactors = F)
+head(b)
+ggplot(b, aes(x = region, y = observations)) +
+stat_summary(fun = mean, geom = "bar") +
+xlab("region") +
+ylab("population") +
+theme_classic()
+b <-  read.table("data.txt", header = T, sep = ",", stringsAsFactors = F)
+head(b)
+ggplot(b, aes(x = region, y = observations)) +
+stat_summary(fun = mean, geom = "bar") +
+xlab("region") +
+ylab("population") +
+theme_classic()
+#2-2 a scatter plot of all of the observations
+ggplot(b, aes(x = region, y = observations)) +
+geom_jitter(size = 1)+
+theme_classic()

answer codes_Lan.R

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+setwd("Desktop/Biocomp_tutorial12/")
+library(ggplot2)
+rm(list = ls())
+#1. a scatter plot of those two variables (time and the amount of cumulative drug release)
+a <-  read.table("drug_release.txt", header = T, sep = "", stringsAsFactors = F)
+head(a)
+ggplot(a,aes(x = hours, y = cumulative_drug_release)) +
+  geom_point(size = 3) +
+  stat_smooth(method = "loess", se=FALSE) +
+  xlab("Time (hour)") +
+  ylab("cumulative drug release (ng)") +
+  theme_classic() +
+  theme(legend.title=element_blank())
+
+# 2-1 a barplot of the means of the four populations
+b <-  read.table("data.txt", header = T, sep = ",", stringsAsFactors = F)
+head(b)
+ggplot(b, aes(x = region, y = observations)) +
+  stat_summary(fun = mean, geom = "bar") +
+  xlab("region") +
+  ylab("population") +
+  theme_classic()
+
+#2-2 a scatter plot of all of the observations
+ggplot(b, aes(x = region, y = observations)) +
+  geom_jitter(size = 1)+
+  theme_classic()
+
+#2-3 Do the bar and scatter plots tell you different stories? Why?
+# Yes. Population for all groups seem to be the same in the bar plot but they are slightly different from the scatter plot.
+# The reason is that bar plots mainly show the mean values, but less direct for showing the data distribution; instead, scatter plots can directly show the data distribution including outliers, but are hard to see the mean values. 

drug_release.txt

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+hours	cumulative_drug_release
+0	0
+24	565.31
+48	990.06
+72	1330.44
+96	1642.72
+120	1870.39
+144	2081.28
+168	2224.73