User: smyiz

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smyiz20
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3 months, 3 weeks ago
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7 months, 2 weeks ago
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Posts by smyiz

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How can I reorder row clusters using complexheatmap
... the problem is solved. just need to add this parameter: cluster_row_slices = FALSE ...
written 6 months ago by smyiz20
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How can I reorder row clusters using complexheatmap
... I want to change order of clusters on the heatmap using Complex Heatmap package and I used pearson distance method and average method. When I cut the row dendrogram, cluster order is 1,3,2,4. How can I change it to this order :2,1,3,4 clusters = dendextend::cutree(hx, k = 4) co ...
R complexheatmap written 6 months ago by smyiz20 • updated 6 months ago by Kevin Blighe53k
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Comment: C: plotting problem with loop in R
... I think, your formulas equal ( x * y) / sqrt(sum(x)^2 * sum(y)^2. In uncentered correlation, it should be started with sum(x*y) ...
written 7 months ago by smyiz20
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Comment: C: plotting problem with loop in R
... Thanks, but I didn't quite get it. Do you mean I need to change v1 <- X[ , i] to v1 <- distMat[ ,i] ...
written 7 months ago by smyiz20
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Comment: C: plotting problem with loop in R
... "cor" function wants only these methods: "pearson", "kendall", "spearman", I wanna use uncentered-pearson ...
written 7 months ago by smyiz20
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Comment: C: plotting problem with loop in R
... > ncol(X) [1] 18 > nrow(X) [1] 3173 > n [1] 3173 ...
written 7 months ago by smyiz20
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Comment: C: plotting problem with loop in R
... Thanks for your reply but I am getting this error: Error in X[, i] : object of type 'closure' is not subsettable ...
written 7 months ago by smyiz20
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Comment: C: plotting problem with loop in R
... I call "dev.off()" and the output reads "null device". the plot is not generated :( ...
written 7 months ago by smyiz20
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plotting problem with loop in R
... I am trying to calculate the correlation coefficient and prepare distance matrix and draw a plot of clustering. I am stuck in plotting. Here is my script: coef <- function(x,y){ a <- sum(x * y) / sqrt(sum(x)^2 * sum(y)^2) return(a) } distance <- function ...
R plot written 7 months ago by smyiz20
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how to normalize row counts before drawing heatmap?
... I have raw counts and edgeR differential expression results and want to draw a heatmap with logFC value. I have 12 groups, two cell lines with triplicate total and IP. (cell1T1, cell1T2, cell1T3, cell1IP1, cell1IP2, cell1IP3, cell2T1, cell2T2, cell2T3, cell2IP1, cell2IP2, cell2IP3) I want ...
R rna-seq heatmap written 7 months ago by smyiz20

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