Hello,
So I have a excel/txt file that has the genes listed in column1, i have the fold change of these genes in one group in column 2, and another fold change in column 3. I performed DAVID analysis to get the GO terms.
What I am trying to do is to see if I can group the genes into the different GO terms with their associated fold change between column 2 and 3.
Ive been looking online and haven't really been able to find a solution that I can really comprehend.
I tried use Galaxy to input the list myself, but was wondering if there is a way to group them into GO terms before i generate the heatmap.
Sorry I am new to this and thanks for any suggestions
Hello Kevin,
thanks for the reply,
I was wondering how I would go about changing this part of your code:
draw(hmapGSEA + haGenes, heatmap_legend_side="right", annotation_legend_side="right") dev.off()
to just generating a heat map based off of fold change between two different experimental conditions. I've just started to learn R. My toptable has 3 columns (column 1 is the list of genes, column 2 is fold change in one condition, and column 3 is fold change in an another experimental condition). I have about 51 go terms with a lot of overlapping genes that I want to visualize on a heatmap between these two conditions
Thanks for the help and any suggestions!
I see, this function is not really for that type of data - it is more for data coming straight from the DAVID website. Essentially, the input to the
Heatmap()
function is a matrix of1
and0
(1 = gene present in GO term; 0 = gene not present in GO term)