watching your lessons alone, i learned so many other functions in r, that i would have otherwise needed in other analysis. You saved me a ton of minutes of google searching. Again you are the best
Thank you so much Mike!! I followed all of this step by step and my heatmaps turned out be beautiful! You’re a lifesaver, please keep up the good work!!!
Thanks for your easy video. I would like to know the code for making font "bold" in the two groups. I searched on google but neither of code work in this pheatmap function. I can change font size but cannot make "bold".
Hi Mike. Thank you very much for this useful and great tutorial. I was able to reproduce the VolcanPlot but do you have any idea how I can indicate the names of the significant genes on each side? Thank you
Hey Mike! Thankyou for an easy video on plotting. Can you share a piece of code for hierarchical clustering of genes according to expression pattern. Thankyou so much in advance.
I created a volcano plot by enhance volcano.But in the plot instead of showing the gene symbol some kind of number are shown.So how can i solve this problem. EnhancedVolcano(exp1, x = "logFC", y = "adj.P.Val", lab = rownames(exp1), FCcutoff = 0.6, pCutoff=0.01, cutoffLineType = 'twodash', cutoffLineWidth = 0.4, pointSize = 1, legendPosition = 'none', title = "", subtitle = "", caption = "", labSize = 3, ylim = c(0, 6)) + theme_pubr(legend = "none"). exp1 is my dataset and the first column of that dataset is gene symbol.
Hi Mike, thank you for making the video. How do you get your _water and _15psu samples arranged next to eachother? I want to arrange my samples by group. Right now they are not ordered by group in my heatmap. Is there a way to manually arrange and group samples in pheatmap?
Hey, so that ordering was mostly luck and coincidence, but if i wanted to force an order, i'd force it with a python script or even in excel (have to be careful with the whole gene name to date phenomenon though).
@@mikevandewege3007 Good point. I will try and export the sigCount and change the sample order manually outside R. I’m trying to use your code to visualize differential abundance of bacteria between two groups. Although significantly different the samples of each group don’t cluster as nice as with your data. Thanks for the reply!
Hi Mike, thank you for the wonderful explanation. But i have encounter a problem... library(DESeq2) > library(apeglm) > library(htmltools) > library(ggplot2) > setwd("E:/Population Genomics data analysis/Ecotypic_differences/SAM/DEGs/SOR_VS_WOR") > dat info dds
@@shilpisingh9718 I think you would just more or less follow the heatmap guide. I'm basically plotting 3 samples per treatment for 2 different treatments.
watching your lessons alone, i learned so many other functions in r, that i would have otherwise needed in other analysis. You saved me a ton of minutes of google searching. Again you are the best
Thank you so much Mike!!
I followed all of this step by step and my heatmaps turned out be beautiful! You’re a lifesaver, please keep up the good work!!!
Thank you so much for this very helpful resource!!
Thank you for these videos
Thank you for making this video! It was really helpful!
Thank you so much for this great lecture ...
Thanks for the great lecture
you are the best man
Thanks for your easy video. I would like to know the code for making font "bold" in the two groups. I searched on google but neither of code work in this pheatmap function. I can change font size but cannot make "bold".
Hi Mike. Thank you very much for this useful and great tutorial. I was able to reproduce the VolcanPlot but do you have any idea how I can indicate the names of the significant genes on each side? Thank you
Maybe geom_text() can help you out. If not, some other module in ggplot will put text on graphs.
Hey Mike! Thankyou for an easy video on plotting. Can you share a piece of code for hierarchical clustering of genes according to expression pattern. Thankyou so much in advance.
I created a volcano plot by enhance volcano.But in the plot instead of showing the gene symbol some kind of number are shown.So how can i solve this problem.
EnhancedVolcano(exp1, x = "logFC", y = "adj.P.Val",
lab = rownames(exp1),
FCcutoff = 0.6, pCutoff=0.01, cutoffLineType = 'twodash',
cutoffLineWidth = 0.4, pointSize = 1, legendPosition = 'none',
title = "", subtitle = "", caption = "", labSize = 3, ylim = c(0, 6)) +
theme_pubr(legend = "none").
exp1 is my dataset and the first column of that dataset is gene symbol.
I have also made a volcano via Enhanced but my plot is reversed. Do you have any suggestions to solve this problem? Thanks
Was it neccesary to merge? Beacause then later you just pick the 6 first columns, so i didnt really understand that step... Thanks for the video
The info for DEGs and read counts are in different files. I merge so i can filter, but i may only want to plot on a condition.
@@mikevandewege3007 oh okay i think i see it, thanks a lot!!! :D
Hi Mike, thank you for making the video. How do you get your _water and _15psu samples arranged next to eachother? I want to arrange my samples by group. Right now they are not ordered by group in my heatmap. Is there a way to manually arrange and group samples in pheatmap?
Hey, so that ordering was mostly luck and coincidence, but if i wanted to force an order, i'd force it with a python script or even in excel (have to be careful with the whole gene name to date phenomenon though).
Alternatively, if the differences in treatment are really clear, they'll cluster automatically in pheatmap.
@@mikevandewege3007 Good point. I will try and export the sigCount and change the sample order manually outside R. I’m trying to use your code to visualize differential abundance of bacteria between two groups. Although significantly different the samples of each group don’t cluster as nice as with your data. Thanks for the reply!
Hi Mike, thank you for the wonderful explanation. But i have encounter a problem...
library(DESeq2)
> library(apeglm)
> library(htmltools)
> library(ggplot2)
> setwd("E:/Population Genomics data analysis/Ecotypic_differences/SAM/DEGs/SOR_VS_WOR")
> dat info dds
Hey MikE! Thanks for the nice video. Can you please share how to plot up-down regulated genes of two sample with replicates
Like as a heatmap?
@@shilpisingh9718 I think you would just more or less follow the heatmap guide. I'm basically plotting 3 samples per treatment for 2 different treatments.