User: CodeAway

gravatar for CodeAway
CodeAway50
Reputation:
50
Status:
New User
Location:
Last seen:
1 year, 3 months ago
Joined:
2 years, 6 months ago
Email:
r******@gmail.com

Posts by CodeAway

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
381
views
1
answers
Comment: C: Input genes for GSVA
... Thank you Robert!  I appreciate your response.     ...
written 19 months ago by CodeAway50
1
vote
1
answer
381
views
1
answer
Input genes for GSVA
... Hello All, I would like to know what exactly should be the set of genes that go as input in the expression matrix to GSVA (not the gene set but the expression matrix). I am working particularly within the context of single-cell data, and have marker genes for two groups. I would like to find out th ...
gsva gene expression matrix written 19 months ago by CodeAway50 • updated 19 months ago by Robert Castelo2.3k
1
vote
0
answers
951
views
0
answers
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$cluster), which="row", col = list(Cluster = ttxx)) Now it works. ...
written 2.2 years ago by CodeAway50
0
votes
0
answers
951
views
0
answers
Comment: C: Automatic color assignment for annotations on ComplexHeatmap
... Further to my post above, I tried doing this: ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row", col = list(Cluster = colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks$cluster)))) ) But I got the following error: E ...
written 2.2 years ago by CodeAway50
3
votes
0
answers
951
views
0
answers
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 2.2 years ago by CodeAway50
1
vote
3
answers
10k
views
3
answers
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 2.5 years ago by CodeAway50
1
vote
3
answers
10k
views
3
answers
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 2.5 years ago by CodeAway50
0
votes
2
answers
1.6k
views
2
answers
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 2.5 years ago by CodeAway50
0
votes
2
answers
1.6k
views
2
answers
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 2.5 years ago by CodeAway50 • updated 19 months ago by angela.ubn0

Latest awards to CodeAway

Popular Question 15 months ago, created a question with more than 1,000 views. For Change point size and remove outline in scater's plotPCA

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 283 users visited in the last hour