Hi!
I would like to plot the log2FC of 80 genes of a time course experiment (from 0 to 168hrs) as line plot. So originally my dataset has the genes in rows and the log2FC per time point in column but looking a way to do it I found this post so I transposed the dataset obtaining:
A tibble: 11 x 80
timepoints MAPK10 PCSK2 PCSK5 APBA1 CACNA1D MME ITPR3 LOC395985
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0 -1.10 -2.91 -1.00 -0.980 -0.575 -0.573 0.849 1.27
2 24 -1.86 -4.76 -1.72 -1.60 -2.28 -0.749 0.332 -1.12
3 48 -1.49 -4.42 -1.67 -1.79 -2.39 -0.457 0.120 -0.658
4 54 -0.859 -3.54 -1.30 -1.64 -2.24 -0.128 0.559 0.726
5 60 -1.45 -3.90 -2.20 -1.94 -2.73 0.110 0.155 0.25
But when I try to follow the post (literally exactly the same code) I do not get any plot (not even the line plot for each gene). I checked if there were any NA and if the columns were character (df2 <- df %>% mutate_if(is.character,as.numeric) ) !
What am I doing wrong??
Thank you!
Camilla
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1 answer
Dont know if this plot is what you want:
library(tidyr)
library(dplyr)
library(ggplot2)
test.df <- data.frame(a=seq(1:10),
matrix(nrow = 10,ncol = 80,data = runif(800)))
names(test.df) <- c("timepoints",paste0(rep("gene",80),seq(1:80)))
test.df.long <- test.df %>% pivot_longer(all_of(paste0(rep("gene",80),seq(1:80))))
test.df.long %>%
ggplot(aes(x= timepoints,y=value,color=name)) +
geom_line(aes(group = name))
However, as Chirag said in that old post, for so many genes, its better to use heatmap.
library(pheatmap)
test.trans <- test.df %>% t()
colnames(test.trans) <- paste0("T",test.trans[1,])
test.trans <- test.trans[-1,]
pheatmap(test.trans,
cluster_cols = FALSE,
show_rownames = FALSE)
...and here is the plot
EDIT: The line plot is too big to show.
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