## User: Raivo Kolde

Raivo Kolde50
Reputation:
50
Status:
Trusted
Location:
Boston
Scholar ID:
Last seen:
10 months, 3 weeks ago
Joined:
3 years ago
Email:
r**********@eesti.ee

Postdoctoral scholar at Massachusetts General Hospital.

#### Posts by Raivo Kolde

<prev • 7 results • page 1 of 1 • next >
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... If you have the mygenes variable that is a gene name vector already, then just enter gl = list(MyGeneList = mygenes) and you should be good. ...
written 10 months ago by Raivo Kolde50
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... There is no explicit memory restriction in pheatmap, but it is certainly not optimized for such large heatmaps.  Usually, a heatmap with 50K rows does not make much sense, as the number of vertical pixels available in a typical (or even atypical for that matter) screen is an order of magnitude small ...
written 2.3 years ago by Raivo Kolde50
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... You have to update your version of pheatmap. This feature of giving clustering as a parameter was introduces fairly recently.  ...
written 2.5 years ago by Raivo Kolde50
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... It is a hack but basically you can achieve it like this (starting from full correaltion matrix again)  o = rownames(mat) hc = hclust(as.dist(1 - mat)) mat = mat[hc$order, hc$order] mat[lower.tri(mat)] = NA mat = mat[o, o] pheatmap(mat, cluster_col = hc, cluster_row = hc) ...
written 2.5 years ago by Raivo Kolde50
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... Then you have to cluster the data before you assign some values NA. For example assuming that mat is full correlation matrix you can do the following hc = hclust(as.dist(1 - mat)) mat = mat[hc$order, hc$order] mat[lower.tri(mat)] = NA pheatmap(mat, cluster_col = F, cluster_row = F) ...
written 2.5 years ago by Raivo Kolde50
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... It probably will work if you remove quotation marks around NA. Also turn off the clustering of rows and columns to see nice triangular plot. ...
written 2.5 years ago by Raivo Kolde50
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585
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... GOsummaries actually can handle the Entrez ids as well, although the feature is not well documented. With the numeric IDs gProfiler (http://biit.cs.ut.ee/gprofiler/) that is used by GOsummaries does not know to which database these IDs correspond to, but you can specify it from the web interface. Th ...
written 3.0 years ago by Raivo Kolde50

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