1.Box plots

1.1 Basic box plot

df$cyl <- as.factor(df$cyl)
head(df)

##                    mpg cyl    wt
## Mazda RX4         21.0   6 2.620
## Mazda RX4 Wag     21.0   6 2.875
## Datsun 710        22.8   4 2.320
## Hornet 4 Drive    21.4   6 3.215
## Hornet Sportabout 18.7   8 3.440
## Valiant           18.1   6 3.460

ggplot(df, aes(x=cyl, y=mpg)) + 
  geom_boxplot(fill="gray")+
  labs(title="Plot of mpg per cyl",x="Cyl", y = "Mpg")+
  theme_classic()

1.2 Change continuous color by groups

ggplot(df, aes(x=cyl, y=mpg, fill=cyl)) + 
  geom_boxplot()+
  labs(title="Plot of mpg per cyl",x="Cyl", y = "Mpg") +
  scale_fill_brewer(palette="Blues") + 
  theme_bw()

1.3 Box plot for GO results

df7$Term <- sapply(strsplit(as.vector(df7$Term),'~'),'[',2)
head(df7)

#          Category                                                         Term Count       X.      PValue
#1 GOTERM_BP_DIRECT                               chemical synaptic transmission     6 4.651163 0.003873106
#2 GOTERM_BP_DIRECT                                                cell motility     3 2.325581 0.007016402
#3 GOTERM_BP_DIRECT negative regulation of intrinsic apoptotic signaling pathway     3 2.325581 0.011455205
#4 GOTERM_BP_DIRECT                protein N-linked glycosylation via asparagine     3 2.325581 0.014940498
#5 GOTERM_BP_DIRECT            positive regulation of androgen receptor activity     2 1.550388 0.017976476
#6 GOTERM_BP_DIRECT                               photoreceptor cell maintenance     3 2.325581 0.024198625
#                                                                                                                   Genes
#1 ENSMUSG00000032360, ENSMUSG00000020882, ENSMUSG00000000766, ENSMUSG00000020745, ENSMUSG00000029763, ENSMUSG00000066392
#2                                                             ENSMUSG00000022665, ENSMUSG00000043850, ENSMUSG00000031078
#3                                                             ENSMUSG00000095567, ENSMUSG00000036199, ENSMUSG00000030421
#4                                                             ENSMUSG00000031232, ENSMUSG00000028277, ENSMUSG00000024172
#5                                                                                 ENSMUSG00000038722, ENSMUSG00000028964
#6                                                             ENSMUSG00000037493, ENSMUSG00000043850, ENSMUSG00000020212
#  List.Total Pop.Hits Pop.Total Fold.Enrichment Bonferroni Benjamini       FDR
#1        110      172     18082        5.734249  0.8975036 0.8975036  5.554012
#2        110       21     18082       23.483117  0.9839676 0.8733810  9.848665
#3        110       27     18082       18.264646  0.9988443 0.8950571 15.604073
#4        110       31     18082       15.907918  0.9998546 0.8901964 19.881092
#5        110        3     18082      109.587879  0.9999763 0.8811197 23.441198
#6        110       40     18082       12.328636  0.9999994 0.9089683 30.281607

ggplot(df7) + geom_bar(stat="identity", width=0.6, aes(Term,Fold.Enrichment, fill=-1*log10(PValue)),colour="#1d2a33") + 
  coord_flip() +
  scale_fill_gradient(low="#e8f3f7",high="#236eba")+
  labs(fill=expression(-log10_Pvalue), x="GO Terms",y="foldEnrichment", title="GO Biological Process") +
  theme_bw() +
  theme(plot.title = element_text(hjust = 0.5))  +
  theme(axis.title.x =element_text(size=16), 
        axis.title.y=element_text(size=14)) +
  theme(axis.text.y = element_text(size = 10,face="bold"),
        axis.text.x = element_text(size = 12,face="bold"))

Reference: http://www.sthda.com/english/wiki/ggplot2-box-plot-quick-start-guide-r-software-and-data-visualization