Question: Problem with heatmap by ComplexHeatmap
gravatar for Luiz
22 months ago by
Luiz0 wrote:

Good morning!

I'm trying to produce a heatmap only with my DGE from NOISeq.

I'm working with ComplexHeatmap, and already produced a nice looking heatmap with annotations (pipeline below) but,  the heatplot produced utilize random transcripts between 1 and 1324 (my number of DGE) even if they're not significant (prob <0.05)

My pipeline is:

mat = mynoiseq2[sample(nrow(mynoiseq.deg), nrow(mynoiseq.deg)), colnames(mynoiseq2)]
mat_scaled = t(apply(mat, 1, scale))
hb = HeatmapAnnotation(barplot = anno_boxplot(mat2))
hc = HeatmapAnnotation(barplot = anno_points(rnorm(10))
Heatmap(mat_scaled, col=rev(rainbow(10)), show_row_names=FALSE, cluster_columns=FALSE, cluster_rows=FALSE, bottom_annotation = hc, top_annotation=hb)

Where "mynoiseq2"  is my total data.frame with groups and reads (3774 transcripts), mynoiseq.deg is my DGE with groups mean, theta, prob and LFC values.

i'm trying to plot a heatmap based on value of P + DGE + Column names, i already make something like that on edgeR with:

heatmap(log(normCounts[de[1:352],]+1),Colv=NA, ylab="Genes", labRow=F, margins=c(2,2))

Where 352 is the number of my DGE and de is my data.frame with them. With DESeq2, i make this process through:

de <- rownames(res[res$padj<0.05 & !$padj), ])
de_mat <- assay(rld)[de,]
heatmap(de_mat, Colv=NA, ylab="Genes", labRow=F, margins=c(2,2))

But now i need a more complex heatmap with the same criterea (only DGEs plotted with P or even reads + log where i can show the pattern of expression from DGE)

TY for your attention!

noiseq rstudio complexheatmap • 448 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by Luiz0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 308 users visited in the last hour