User: CodeAway

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CodeAway20
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Posts by CodeAway

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Automatic color assignment for annotations on ComplexHeatmap
... I solved this myself as follows: ttxx <- colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks$cluster))) names(ttxx) <- levels(top20mrks$cluster) ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row", col = list(Cluster = ttxx)) Now it works. ...
written 9 weeks ago by CodeAway20
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Comment: C: Automatic color assignment for annotations on ComplexHeatmap
... Further to my post above, I tried doing this: ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row", col = list(Cluster = colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks$cluster)))) ) But I got the following error: E ...
written 10 weeks ago by CodeAway20
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Automatic color assignment for annotations on ComplexHeatmap
... Hello All, I love the ComplexHeatmap package, and have been using it to make some gene expression heatmaps.  If I wish to add row annotations for genes, with each gene belonging to one of 10 clusters, how do I make automatic color assignments to the groups instead of giving them as a list manually? ...
complexheatmap written 10 weeks ago by CodeAway20
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Comment: C: New function lfcShrink() in DESeq2
... Thanks, Michael.  Yes, that makes it clear.  So, in short, for regular bulk RNAseq data, would you recommend using the shrunken LFCs vs not using it?  As far as I understand, the main reason you decided to change the default in DESeq2, is for types of data other than bulk RNAseq, correct?  Thanks a ...
written 5 months ago by CodeAway20
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Answer: A: New function lfcShrink() in DESeq2
... Thank you very much, Michael, for the clarification, as I was looking for this answer and was getting confused about the removal of the  shrinkage feature by default from DESeq2.  So, would you say that for regular bulk RNAseq, we should use this shrinkage feature by default as usual like in the ol ...
written 5 months ago by CodeAway20
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Comment: C: Change point size and remove outline in scater's plotPCA
... Thanks, James.  I am actually not using "size_by", so that is left to default. I was able to change the colors of the points as below: ppcah <- plotPCA(sce, pca_data_input="pdata", colour_by="sample_type", shape_by=NULL) +   scale_fill_manual(values=c("WT"="blue", "R172K"="red")) +   labs(fil ...
written 6 months ago by CodeAway20
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Change point size and remove outline in scater's plotPCA
... Hello All, Just need a quick help, with regards to the plotPCA function of the "really excellent" scater package, that I am using for single-cell RNAseq analysis of 10X data.  I wish to change the size of the points and also remove the gray outlines that currently appear around the points. I tried ...
rnaseq single-cell scater written 6 months ago by CodeAway20 • updated 6 months ago by James W. MacDonald45k

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