CODEWITHSUNDEEP
rif-statementcolorsggplot2scatter-plot
Chris Dias
Chris Dias

Reputation: 87

Scatterplot - multiple colours for "if", "and" conditions

I need to attribute color in a scatterplot where I have multiple conditions. The file is df below. I am plotting Tissue1 vs Tissue2 values. I would like to colour as follows: 

pvalue1 AND pvalue2 < 0.1 = "yellow"
pvalue1 ≤ 0.1 = "green" (if pvalue2 >0.1 or NA)
pvalue2 ≤ 0.1 = "red" (if pvalue1 >0.1 or NA)
(all other = "grey")

df:

rowname Tissue1 pvalue1 Tissue2 pvalue2
gene1   1.3 0.7 1.6 0.09
gene2   -0.9    0.07    -0.7    0.065
gene3   2   0.9 1.65    0.9
gene4   1.7 0.07    1.6 0.09

I am plotting Tissue1 vs Tissue2 using ggplot:

ggplot(data=data.frame(x=df$Tissue1,y=df$Tissue2), 
       aes(x,y)
       )+ geom_point(col="grey30") + 
          geom_abline(stat = "abline", colour = "red", size = 1) + 
          xlab("foldchange Tissue1") + ylab("foldchange Tissue2")

I have tried creating factors, but haven't been able to add them with the ifelse function.

Sig1 <- subset(df, df$pvalue1< 0.1)
Sig2 <- subset(df, df$pvalue2 < 0.1)

I'd appreciate some help with this. Thanks!

Upvotes: 0

Views: 1070

Answers (1)

Roland
Roland

Reputation: 132864

DF <- read.table(text = "rowname Tissue1 pvalue1 Tissue2 pvalue2
                 gene1   1.3 0.7 1.6 0.09
                 gene2   -0.9    0.07    -0.7    0.065
                 gene3   2   0.9 1.65    0.9
                 gene4   1.7 0.07    1.6 0.09", header = TRUE)

#the order of the following lines is important
DF$col <- "grey"
DF[!is.na(DF$pvalue1) & DF$pvalue1 <= 0.1 , "col"] <- "green"
DF[!is.na(DF$pvalue2) & DF$pvalue2 <= 0.1 , "col"] <- "red"
DF[!is.na(DF$pvalue1) & !is.na(DF$pvalue2) & 
   DF$pvalue1 < 0.1 & DF$pvalue2 < 0.1, 
   "col"] <- "yellow"

library(ggplot2)
ggplot(DF, aes(x = Tissue1, y = Tissue2, color = col)) + 
  geom_point() + 
  geom_abline(stat = "abline", colour = "red", size = 1) + 
  xlab("foldchange Tissue1") + ylab("foldchange Tissue2") +
  scale_color_identity()

Upvotes: 4

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