User: Zuguang Gu

gravatar for Zuguang Gu
Zuguang Gu170
Reputation:
170
Status:
Trusted
Location:
Germany / Heidelberg / DKFZ
Website:
http://jokergoo.github...
Last seen:
3 weeks, 4 days ago
Joined:
4 years, 5 months ago
Email:
z***@dkfz.de

Posts by Zuguang Gu

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Error: node stack overflow when trying to plot large dataset using Complexheatm
... Now I add a new argument `jitter` in `Heatmap()` which internally adds random shift to the original matrix. The matrix is only modified when making the dendrograms. The heatmap bodies and the legends are not affected: ```r m = as.matrix(new_df) Heatmap(m, show_row_names = FALSE, jitter = TRUE) ``` ...
written 25 days ago by Zuguang Gu170
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Answer: A: Error: node stack overflow when trying to plot large dataset using Complexheatm
... I cannot solve this problem, but you can add small random values to the original matrix to make no duplicated rows: ```r m = as.matrix(new_df) m = m + runif(length(m), min = 0, max = 1e-10) Heatmap(m, show_row_names = FALSE) ``` To control the legend, set proper values in `heatmap_legend_param` a ...
written 26 days ago by Zuguang Gu170
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Comment: C: Error: node stack overflow when trying to plot large dataset using Complexheatm
... I find a similar case when making heatmaps with too many identical rows with gplots package. https://stackoverflow.com/questions/16559250/error-in-heatmap-2-gplots ...
written 26 days ago by Zuguang Gu170
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Comment: C: Error: node stack overflow when trying to plot large dataset using Complexheatm
... It is because you have too many rows which are identical. The internal function `ComplexHeatmap:::grid.dendrogram()` that draws the dendrogram can handle a matrix with a few identical rows, but it gives errors with too many of that. I will look at this and try to fix it soon. ...
written 26 days ago by Zuguang Gu170
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Comment: C: bam files to hilbert curve
... Sorry, it should be ```r hc = GenomicHilbertCurve(chr = "chr1", level = 5) hc_points(hc, reads, gp = gpar(col = "red")) ``` ...
written 29 days ago by Zuguang Gu170
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Comment: C: bam files to hilbert curve
... Value for `background` argument should contain ranges of chromosomes. In your code, I think `reads` contains the mapped regions that needs to be visualized. Try: ```r hc = GenomicHilbertCurve(chr = "chr1", level = 5) hc_points(hc, reads, col = "red") ``` ...
written 29 days ago by Zuguang Gu170
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Answer: A: bam files to hilbert curve
... You missed a comma here: ``` hc = GenomicHilbertCurve(chr = "chr1", background = reads level = 5, ~~~~ <--- ``` ...
written 29 days ago by Zuguang Gu170
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Comment: C: Handle missing values in the z-score matrix while plotting heatmap in the Comple
... `m` is your matrix (your `mat_marix`). What you did in the `for` loop basically is the same as the `apply()` function. ...
written 4 weeks ago by Zuguang Gu170
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Answer: A: Handle missing values in the z-score matrix while plotting heatmap in the Comple
... try: ``` m2 = t(apply(m, 1, function(x) (x - mean(x, na.rm = TRUE))/sd(x, na.rm = TRUE))) Heatmap(m2) ``` ...
written 4 weeks ago by Zuguang Gu170
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Answer: A: Why is the rGREAT's available ontology with category = "Pathway Data" not workin
... I updated rGREAT for the GREAT version 4.0.4 which is default in current rGREAT. For GREAT version 4.0.4, less ontologies are supported and also note it works with hg38. So if you want to use the ontologies in version 3, specify as `submitGreatJob(..., version = '3.0.0')` ...
written 5 weeks ago by Zuguang Gu170

Latest awards to Zuguang Gu

Scholar 12 weeks ago, created an answer that has been accepted. For A: Combining ComplexHeatmap with other plot types
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: ComplexHeatmap removes row labels if annotation is added
Scholar 23 months ago, created an answer that has been accepted. For A: Combining ComplexHeatmap with other plot types
Scholar 23 months ago, created an answer that has been accepted. For A: Make UpSet function display numbers above the bars
Scholar 4.1 years ago, created an answer that has been accepted. For A: Combining ComplexHeatmap with other plot types

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