Dear All,
I am using ggplot2's generate plots for my RNASeq data.
I would like to plot the genes (Gene_name column), one beside the other in the below dataframe.
Here is the sample data with first 20 rows.
Gene_name Chr log2FoldChange padj significant row
gene1 1 1.291089929 0.545016613 no 1
gene2 1 0.873801059 0.588763458 no 2
gene3 1 0.044171969 0.991428121 no 3
gene4 1 2.105103925 0.017808512 yes 4
gene5 1 0.328333094 0.863293666 no 5
gene6 1 1.174288096 0.150119569 no 6
gene7 1 0.247936928 0.840785644 no 7
gene8 1 0.731217106 0.634092244 no 8
gene9 2 -1.622041186 3.14E-13 yes 9
gene10 2 0 0 no 10
gene11 3 -0.839189648 0.000227869 yes 11
gene12 3 0 0 no 12
gene13 4 -1.31624802 2.26E-08 yes 13
gene14 4 -1.2192487 1.82E-05 yes 14
gene15 4 -0.88556427 0.006486725 yes 15
gene16 5 -0.509988484 0.19660206 no 16
gene17 5 -0.292624116 0.670924418 no 17
gene18 5 -1.509072999 1.20E-06 yes 18
gene19 6 0 0 no 19
gene20 7 -0.766677533 0.122287312 no 20
gene21 8 0.269640649 0.804083309 no 21
When I am plotting using the below command it is giving X axis GeneName and y axis logFoldChange. Since I am using GeneName as x axis aesthetic it is giving all GeneNames on x-axis, but i would like to have unique values of chromosome names (Chr column) rather than GeneNames on X-axis. And also I want to highlight genes that has "yes" in significant column.
I am using the below R code to do that
p = ggplot(data = testDE, mapping = aes(x=reorder(Genename, row), y=log2FoldChange)) +
geom_point(aes(col= significant))+
scale_color_manual(values=c("black", "red"))
I would like to plot aes(x=reorder(Genename, row) but I want x axis text as chromosomes rather than Gene names. When I plot this, it is giving dark black line as x-axis labels because i have more number of genes. Could you please help me to get unique values Chr 1 to 22 rather than Gene names on x axis?
Thanks In Advance Fazulur Rehaman (edited: for formatting)
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written
by
vrehaman •
Maybe facet by chromosomes:
testDE <- read.table(text = "Gene_name Chr log2FoldChange padj significant row
gene1 1 1.291089929 0.545016613 no 1
gene2 1 0.873801059 0.588763458 no 2
gene3 1 0.044171969 0.991428121 no 3
gene4 1 2.105103925 0.017808512 yes 4
gene5 1 0.328333094 0.863293666 no 5
gene6 1 1.174288096 0.150119569 no 6
gene7 1 0.247936928 0.840785644 no 7
gene8 1 0.731217106 0.634092244 no 8
gene9 2 -1.622041186 3.14E-13 yes 9
gene10 2 0 0 no 10
gene11 3 -0.839189648 0.000227869 yes 11
gene12 3 0 0 no 12
gene13 4 -1.31624802 2.26E-08 yes 13
gene14 4 -1.2192487 1.82E-05 yes 14
gene15 4 -0.88556427 0.006486725 yes 15
gene16 5 -0.509988484 0.19660206 no 16
gene17 5 -0.292624116 0.670924418 no 17
gene18 5 -1.509072999 1.20E-06 yes 18
gene19 6 0 0 no 19
gene20 7 -0.766677533 0.122287312 no 20
gene21 8 0.269640649 0.804083309 no 21", header = TRUE, stringsAsFactors = FALSE)
library(ggplot2)
# pre-order the rows by chromosome and gene start positions?
# I am guessing that is what "row" column is doing?
testDE$Gene_name <- factor(testDE$Gene_name, levels = testDE$Gene_name)
ggplot(testDE, aes(x = Gene_name, y = log2FoldChange)) +
geom_point(aes(col = significant)) +
scale_color_manual(values = c("black", "red")) +
facet_grid(.~paste0("Chr", Chr), scales = "free_x") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.3, hjust=1))
Dear @zx8754,
Thanks a lot for your quick response & solution to the plot. I used the code above & generated plot. It gives me plot exactly I want.
Thanks again. Fazulur Rehaman
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Do you want it this way?
if so, please replace
Gene_namewithchr(reorder(Chr, row)).If you want same plot (as in OP), but for each chromosome separate, do a facet wrap:
facet_wrap( ~ Chr, ncol = length(unique(testDE$Chr)), scales = "free"). This would plot X and Y axis on free scale. However, if you want only x-axis free, then changescales="free_x"