NGSseq heatmap RStudio
0
0
Entering edit mode
4.7 years ago
aroso491 • 0

Hello everyone and thanks for your time in advance.

I'm trying to complete a practical exercise that I am meant to do for my MSc in Bioinformatics. I have asked my lecturer, which due to the recent lockdown has informed me that unfortunately he will not be able to answer queries anytime soon. I am trying to understand this bit of the practical so that I can get on with my final assignment which involves the use of heatmaps in a similar fashion, and I only have 6 days for that.

Introduction done, I hope any of you can help me understanding what is the right direction.

My issue is as follows: I'm making an expression heatmap with the z-scores of two sample groups, gut and node, for some significantly different genes. My basic table includes a column of string chars (codes for genes) plus another 6 columns with the differential expression numbers for each replica, three for gut, three for the node.

Original table - not zScores significance_DG=master_file[which(master_file$sig_mL_DP_LP=="TRUE"),] significance_DG_table=significance_DG[c(1,8:10,14:16)]

sig_zTrans=significance_DG_table
sig_zTrans[,c(2:7)] = t(scale(t(sig_zTrans[,c(2:7)]), center=TRUE, scale = TRUE))
sig_DG_zScore=data.frame(sig_zTrans)
melted_sig_DG_preorder=melt(sig_DG_zScore, na.rm=T)
ggplot(melted_sig_DG_preorder, aes(x=variable, y=ID, fill=value)) + geom_tile()

sig_genes_matrix_scaled_na <- na.omit(sig_DG_zScore)
y.dist=Dist(sig_genes_matrix_scaled_na[,c(2:7)],method = "spearman")
y.cluster=hclust(y.dist,method="average")
y.dd=as.dendrogram(y.cluster)
y.dd.reordered=reorder(y.dd,0,FUN="average")
y.order=order.dendrogram(y.dd.reordered)
y.orderlabeled=sig_genes_matrix_scaled_na[y.order,]

names=as.factor(sig_genes_matrix_scaled_na[y.order,1])
names = factor(names, levels = names[y.order])
my_data_ordered<-data.frame(name=names, val=y.orderlabeled)
melted_sig_DG=melt(my_data_ordered, na.rm = T)
ggplot(melted_sig_DG, aes(x=variable, y=name, fill=value)) + geom_tile()

Instead of a nice, ordered heatmap, what I am getting is this

Heatmap ggplot after clustering Does anyone have any idea about where am I going wrong?

RNA-Seq heatmap R RStudio ggplot • 1.3k views
ADD COMMENT
0
Entering edit mode

Try ComplexHeatmap R package. It internally handles clustering stuff. You just need to give your expression matrix.

ADD REPLY
0
Entering edit mode

That's brilliant, thank you, will try and let you know if it worked!!

ADD REPLY
0
Entering edit mode

I forgot to add that it worked perfectly in case anyone passes by and wonders if it was worth it or not.

ADD REPLY

Login before adding your answer.

Traffic: 1832 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6