User: qicaibiology

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qicaibiology40
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Posts by qicaibiology

<prev • 80 results • page 1 of 8 • next >
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Comment: C: How to get the order of clustered genes of heatmap.2 to a .csv file?
... Hi Kevlin: Thank you for the link, when I tried to re-do what the code instructed, but I got an error I can't understand. My matrix contains 5 columns, column 1 to column4 are the counts at different stages, while column5 are the differences between colum3 and column1 (which is diff=column3-colum1) ...
written 10 days ago by qicaibiology40
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Comment: C: How to get the order of clustered genes of heatmap.2 to a .csv file?
... Hi Kevin: Is it possible to do the same in ComplexHeat map. I put the above command in Heatmap it throws out a message:" > Error in Heatmap(mydat_2, name = "mat", Rowv = > as.dendrogram(row_clust), : unused argument (Rowv = > as.dendrogram(row_clust)) I read the manual of complexheat ...
written 10 days ago by qicaibiology40
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Comment: C: Boxplot or ggplot
... mydat2 <- tidyr::gather(mydat, key = "stage", value = "new_col", E11, E14, E18, Adult) mydat is a matrix, I chekced all the numbers in E11, E14, E18, Adult are numeric. but got an error: Error in gather_(data, key_col = compat_as_lazy(enquo(key)), value_col = compat_as_lazy(enquo(value) ...
written 12 days ago by qicaibiology40
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Boxplot or ggplot
... I am comparing gene expression level across 4 developmental stages: E11, E14, E18, Adult. I have about 800 genes selected. Each genes has a read at these satages. Now I made a matrix: the row name are gene ID, while the column name are the 4 stages. each columns contains the read number. I can easil ...
software error R rna-seq sequencing written 12 days ago by qicaibiology40 • updated 12 days ago by MatthewP620
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custom cluster or split heatmap?
... I begin to use ComplexHeatmap to plot the dymamic change of values across different development stages in R. 1. I started from two dataframe, for example `df_1` and `df_2`, I merged them into `df_3` (`df_3 <- rbind(df_1, df_2)`. I have plot Heatmap on `df_3`, but I want the heatmap to be able ...
software error R rna-seq written 12 days ago by qicaibiology40 • updated 12 days ago by RamRS27k
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Comment: C: barplot is missing in png file after saving
... Right. I did not have code. I ran it in Rstudio. ...
written 12 days ago by qicaibiology40
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Comment: C: barplot is missing in png file after saving
... I run the code on Rstudio. on the right corner, there is a image, i just export it as pdf. ...
written 12 days ago by qicaibiology40
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Comment: C: barplot is missing in png file after saving
... Thank you. I exported it from R. ...
written 13 days ago by qicaibiology40
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barplot is missing in png file after saving
... Dear all: I am using ggplot to do a barplot for geneOntology in R. The output is fine. However, I can only see the labeling of the bar in the saved png file. But if I saved it as pdf all the content is shown . How should I adjust the size of the image. My code is: p <- ggplot(data=mydata_ ...
software error R next-gen rna-seq gene written 13 days ago by qicaibiology40 • updated 13 days ago by Kevin Blighe60k
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Comment: C: error in reorder the bars of ggplots
... I saw a lot of people say it will work. But It did not work in my hand. In the end, I use `mutate(Term = fct_reorder(Term, logPValue))` to make it work. I still do not know the reason. ...
written 13 days ago by qicaibiology40

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