User: rpolicastro

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rpolicastro720
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Posts by rpolicastro

<prev • 111 results • page 2 of 12 • next >
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Comment: C: subscript out of bounds in seurat expression matrix
... When you did the marker analysis, what assay and slot did you use? Some of the slots hold all genes that pass quality filtering, while others only hold the top 2-3k most variable genes. ...
written 3 days ago by rpolicastro720
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Comment: C: How to visualize Boxplot with using fold change values in ggplot2 in R
... The [ggpubr library](https://github.com/kassambara/ggpubr) has a convenience function to make a box plot with significance bars. ...
written 3 days ago by rpolicastro720
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Comment: C: heatmap for TCGA kirk data
... You should put the code you are using here so we know what you are doing. Preferably a reproducible example using a smaller chunk of your data. ...
written 3 days ago by rpolicastro720
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... I find that the scRNA-seq dim plots will sometimes melt illustrator as well. I found a handy library, ggraster, that will let you rasterize the points but keep the labels and such as vectors. I figured I would pass this along in case you haven't seen it. ...
written 3 days ago by rpolicastro720
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... That's a really handy wrapper for pheatmap, thanks for sharing! ...
written 4 days ago by rpolicastro720
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... ComplexHeatmap has a [long but detailed vignette](https://jokergoo.github.io/ComplexHeatmap-reference/book/) that you can go through. Your can prepare your count matrix with this code. Put the genes you want to include the the genes vector. library("Seurat") counts <- GetAssyData(s ...
written 4 days ago by rpolicastro720
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... If you want to add extra information like tissue and donor, you'll need to extract the metadata and UMI counts from the seurat object, and then construct the heatmap using the ComplexHeatmap library. You can get the counts using the `GetAssayData` function, and the metadata can be accessed with two ...
written 4 days ago by rpolicastro720
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... Seurat has a function `DoHeatmap` that will make a heatmap based on the given features and clusters. ...
written 4 days ago by rpolicastro720
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Answer: A: How to visualize Boxplot with using fold change values in ggplot2 in R
... You first need to Convert your data from wide to long format. library("tidyverse") df <- df %>% select(!ends_with("p_val")) %>% pivot_longer(ends_with("FC"), names_to="condition", values_to="fc") > head(df, 5) # A tibble: 5 x 3 Genes condition ...
written 4 days ago by rpolicastro720
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Comment: C: How to sum the genewise counts in edgeR ?
... Thanks, glad to hear my code snippets are helping people! The format you see is the result of the `dput` function being run on a data.frame. It's a way to share a longer data.frame (or most other types of R objects) in a slightly more condensed format. I usually wouldn't use dput in my actual code, ...
written 4 days ago by rpolicastro720

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