Boxplot/bargraph for expression data using ggplot2

Question

[1769mkc]

My data frame

gene    WT            ATRA                VD3
INO80   -1.522663774    0             -0.7068400406
CHD2    1.5314010666    -1.9582412148 -0.1891538235
CHD7    1.1916322634    0              2.0417385999
HELLS   4.804731294     0             -0.0810994075

. I would like to put std.deviation and std.error of mean in my final bar graph

Any help or suggestion would be highly appreciated

[salamandra]

to do the error bars more than one value per condition is needed follows just the code for the barplots:

a <- data.frame(WT=c(-1.522663774, 1.5314010666, 1.1916322634, 4.804731294), ATRA=c(0, -1.9582412148, 0, 0), VD3=c(-0.7068400406, -0.1891538235, 2.0417385999, -0.0810994075), stringsAsFactors = F)
row.names(a) <- c("INO80", "CHD2", "CHD7", "HELLS")
a <- t(a)
barplot(a, names.arg=colnames(a), beside=T, legend.text = T)

[1769mkc]

yes it worked thanks a lot.Can you show me whats wrong with my code if I try that in ggplot2?

[Devon Ryan]

It's difficult to interpret what your actual problem is. If you need to add error bars in ggplot2, then it's the geom_errorbar() function.

[1769mkc]

okay now i have edited my question since I had issues with CHD2 gene .

My issues is I would like to plot the expression of 4 gene in WT ,in ATRA and VD3. So basically i have to melt and reshape the data and plot bar graph that;'s it?

[Devon Ryan]

See the gather() function in tidyr.

[1769mkc]

library(tidyr)
library(dplyr)
library(ggplot2)
dat <- read.csv('gene_boxplot.csv')
head(dat)
mdat = dat%>% gather(key = sample, value = val, -gene)
head(mdat)
 gene      sample        val


 INO80    WT -1.5226638
 CHD2     WT  1.5314011
 CHD7     WT  1.1916323


  HELLS     WT  4.8047313
  SMARCD3   WT -0.5394756


  INO80   ATRA  0.0000000






p <-ggplot(mdat, aes(gene, val))
p +geom_bar()

I get this error Error: stat_count() must not be used with a y aesthetic.

[Joe]

This isn't really a bioinformatics question. This is just that you need to go and follow a walkthrough/tutorial online for how to format the data for ggplot barplots (I'd be the first to admit that ggplot's errors aren't the most discernable).