User: Raivo Kolde

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Raivo Kolde50
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Location:
Boston
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Google Scholar Page
Last seen:
3 months, 3 weeks ago
Joined:
2 years, 5 months 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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Answer: A: Properly assigning gene list objects in GOsummaries
... 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 3 months ago by Raivo Kolde50
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Answer: A: R crash when matrix nrows exceeds 45000 using pheatmap/heatmap.2
... 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 20 months ago by Raivo Kolde50
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Comment: C: Upper triangular matrix heatmap using pheatmap package
... You have to update your version of pheatmap. This feature of giving clustering as a parameter was introduces fairly recently.  ...
written 23 months ago by Raivo Kolde50
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Comment: C: Upper triangular matrix heatmap using pheatmap package
... 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 23 months ago by Raivo Kolde50
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Comment: C: Upper triangular matrix heatmap using pheatmap package
... 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 23 months ago by Raivo Kolde50
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Comment: C: Upper triangular matrix heatmap using pheatmap package
... 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 23 months ago by Raivo Kolde50
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Answer: A: Package ‘GOsummaries’ --- ENTREZID does not work
... 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 2.5 years ago by Raivo Kolde50

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