Make a Heatmap on R Studio

Catered to those without R experience. Using the heatmap.2 function in the gplots R-package.

[sebastianbenitez]

I don't know you but I love your voice. Thanks for the tutorial!

[khushgg]

Nice introduction and well explained tutorial.

[pauladaluzhenriquez]

you helped me so freaking much, thank you!

[AqleemAbbas]

I have tried your protocol, all is good, however I could not find color key and histogram values in my case, I mean relative abundance scale top left in your graph

[musicaorion]

Really very nice explanation. Thanks so much.

[dhurjhotisaha]

Hi, I liked your demonstration. Just one query - I couldn't remove the dendrogram using Rowv = NULL, Colv=NULL or keep.dendro = FALSE commands. Do you have any suggestions? BTW I was using heatmap not heatmap.2

[theanalyst]

i cant find "heatmap.2" in my R but only "heatmap" and so it gives error and I cant get heapmap. Why is it like that?

[romennaorem]

In your script, there is no script for separating between the cells with some gap of white lines. How to separate between the cells with gaps?

[cts]

Hey, thanks for the video, I'm a complete novice that's having a lot of difficulty though. Right a 6:18 is there a reason why the column "Gene" shows up all the way to the left (it is all red)? I'm having the same problem making my heatmap -- R is making a column that shouldn't be there and I can't figure out how to remove it. When I try re-importing like you did at 7:33, it doesn't disappear when I do it like it did for you. I'm using R studio for Windows though and my import menu isn't quite the same as what you have. I can't pick Row Names using the first column in this version for windows, my only option is to use 'the first row as names'.

[LGARCIA]

Helo Leah, thanks for the great class. I have a simple doubt, in my heat map, i can not do the software read my colum names, they put "NA" in the place. The message error is:

>>Missing column names filled in: 'X1' [1]

You can help me? Thanks for your attention.

[acharyaaviseka]

Hello Ms. leah, I am new to use R studio and I have a .csv file with gene function and fold and  I want to make Venn diagram I don't know how to do it can you please help.

[vassiasal]

Very nice introduction and hands-on tutorial thank you! I have some microarray data which I normalized with the limma package and I want to use the p-value from the new file produced containing all the statistics, to filter down and thus create my heatmap. Because otherwise, my matrix file is very large to produce the heatmap. Any suggestions on how to do that?

[benjaminleyton]

I have a question, I can't install gplots but I found the packages "ggplots2" . What is the difference between both?

[Nisab]

i spent hours on a heatmap, then watched this video, found that i was using x <- as.matrix instead of data.matrix

[souradeepaghosh]

What do you mean by margins 10, 12? What does it signify?

[saumyasarkar]

x<- read.csv("SarkarHeat.csv", check.names = FALSE)
> y<-data.matrix(x)
> heatmap.2(y, main = "Sample", trace = "none", margins = c(10, 12))
Error in .External.graphics(C_layout, num.rows, num.cols, mat, as.integer(num.figures), :
invalid graphics state

what does this error mean?

[sadiasalam]

Hello Leah!
Thanks for the video. I just have one problem. How can I change my Row name in the plot?

[kimtu]

Thank you for the video. I have problems with launching "gplots" in Rstudio, the warning message is:
Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:


lowess


Warning message:

package ‘gplots’ was built under R version 3.5.3
Can you please help me to fix that?

[seohyeongkim]

Hi Leah, Thank you for your nice explain.
Actually, I can't change the numeric matrix to my species gene's name. How can I change?

[kyshark]

Hi Leah, thanks for the video. Any chance you could upload the csv file?