User: Zuguang Gu

gravatar for Zuguang Gu
Zuguang Gu180
Reputation:
180
Status:
Trusted
Location:
Germany / Heidelberg / DKFZ
Website:
http://jokergoo.github...
Last seen:
3 weeks, 2 days ago
Joined:
4 years, 6 months ago
Email:
z***@dkfz.de

Posts by Zuguang Gu

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Handle missing values in the z-score matrix while plotting heatmap in the Comple
... It is because, for each gene, you only have two values. ...
written 23 days ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 11 weeks ago by Zuguang Gu180
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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 12 weeks ago by Zuguang Gu180
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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 12 weeks ago by Zuguang Gu180

Latest awards to Zuguang Gu

Scholar 4 months ago, created an answer that has been accepted. For A: Combining ComplexHeatmap with other plot types
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: ComplexHeatmap removes row labels if annotation is added
Scholar 2.1 years ago, created an answer that has been accepted. For A: Combining ComplexHeatmap with other plot types
Scholar 2.1 years ago, created an answer that has been accepted. For A: Make UpSet function display numbers above the bars
Scholar 4.2 years ago, created an answer that has been accepted. For A: Combining ComplexHeatmap with other plot types

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