data <-read.table("box_plots_mtcars.txt",header=T,sep="\t")
df <- data[, c("mpg", "cyl", "wt")]
df2 <-read.table("histogram_plots.txt",header=T,sep="\t")
df3 <- read.table("volcano_plots.txt", header=TRUE)
df4 <- read.table("manhattan_plots_gwasResults.txt",header=T,sep="\t")
df5 <-read.table("heatmaps.txt",header=T,sep="\t")
dm <- data.matrix(df5[1:nrow(df5),2:ncol(df5)])
row.names(dm) <- df5[,1]
df6 <- read.table("ballon_plots_GO.txt", header=T, sep="\t")
df7 <- read.table("box_plots_David_GO.txt",header=T,sep="\t")
df7 <- df7[1:10,]
0.3 Install and library packages
install.packages("ggplot2")
library(ggplot2)
install.packages("qqman")
library(qqman)
install.packages("gplots")
library(gplots)
install.packages("pheatmap")
library(pheatmap)
install.packages("scales")
library(scales)
install.packages("reshape2")
library(reshape2)
install.packages("RColorBrewer")
library(RColorBrewer)
install.packages("plyr")
library(plyr)
install.packages("plotrix")
library(plotrix)
If you want to save the plot, please use "pdf(), dev.off()" or "ggsave()". The second one is specific for the ggplot2 package.
pdf("1.1.Basic_boxplot.pdf", height = 3, width = 3)
ggplot(df, aes(x=cyl, y=mpg)) +
geom_boxplot(fill="gray")+
labs(title="Plot of mpg per cyl",x="Cyl", y = "Mpg")+
theme_classic()
dev.off()
#Or
p <- ggplot(df, aes(x=cyl, y=mpg)) +
geom_boxplot(fill="gray")+
labs(title="Plot of mpg per cyl",x="Cyl", y = "Mpg")+
theme_classic()
ggsave("1.1.Basic_boxplot.pdf", plot=p, height = 3, width = 3)