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
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?
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'.
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.
x y 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?
Yes, Solved. One more thing, when the data is uploaded and processed with data.matrix. The data is showing NAs in the Gene column? I am using windows & OS. Any suggestions?
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?
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
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.
That represents the size of the margins on the x and y axis of the plot, or how much cushioning space do you want. It basically allows your x and y labels to have more space, so that they don't get cut off.
there is literally no useful explanation whatsoever. It would have been really cool to go into how the data needs to be organised and why and how to achive that from a crowded data frame instead of just swirling around with the mouse with the words "this is the data", because that type of magically data organisation usually don't work reproducably.
I'm sorry you weren't able to find what you were looking for. This tutorial has a simple goal: how to create a heatmap. So it takes off from a point where the user already has the matrix they want to plot. Perhaps a tutorial you're looking for would go over the R Data Frame and other R Objects. I'm certain there are good resources for this, like DataCamp.
Nice introduction and well explained tutorial.
I don't know you but I love your voice. Thanks for the tutorial!
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
i spent hours on a heatmap, then watched this video, found that i was using x
Really very nice explanation. Thanks so much.
You helped me a lot! Thanks :)
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?
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'.
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.
So i can't have different gene names?
I have a question , I can't install gplots but I found the packages "ggplots2" . What is the difference between both?
ggplot22 is a new version of ggplots
x y 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?
Yes, Solved.
One more thing, when the data is uploaded and processed with data.matrix. The data is showing NAs in the Gene column? I am using windows & OS. Any suggestions?
Thank you for the video
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?
Hello, that warning message comes up when you load gplots normally, so it's not an issue. You don't have to worry!
Hello, that warning message comes up when you load gplots normally, so it's not an issue. You don't have to worry!
Hello, that warning message comes up when you load gplots normally, so it's not an issue. You don't have to worry!
@@leahbriscoe9130 Thank you, I run succesfully
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?
Thanks Leah...Yea I am having similar challenge and it has to do with the species names been replaced by numbers. Please help
Hello Leah. Kindly share the script used in the video. It will be helpful.
I got it. I will give it a go and update you. Thanks.
Thanks Leah...
Awesome! Thanks
Thank you Leah
Hi Leah, thanks for the video. Any chance you could upload the csv file?
Awesome! thanks a lot!
Thank you!
Great 👍
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
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?
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.
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?
you helped me so freaking much, thank you!
What do you mean by margins 10,12? What does it signify?
That represents the size of the margins on the x and y axis of the plot, or how much cushioning space do you want. It basically allows your x and y labels to have more space, so that they don't get cut off.
Thank you so much
Hello Leah!
Thanks for the video. I just have one problem. How can I change my Row name in the plot?
You can change the name by
rowname (x)
i need r automate script
It would be better to paste the link of the code in description
Thanks for the suggestion! Added code for the advanced heatmap from my other video.
@@howtodataviz5786 i will be thankful if you share a link in here. Thank you. And how about microbial abundance bar plot
@@mianadnankakakhel1185 Good idea for the next video! I put the link in the description.
@@howtodataviz5786 thank you
Thank you!
there is literally no useful explanation whatsoever.
It would have been really cool to go into how the data needs to be organised and why and how to achive that from a crowded data frame instead of just swirling around with the mouse with the words "this is the data", because that type of magically data organisation usually don't work reproducably.
I'm sorry you weren't able to find what you were looking for. This tutorial has a simple goal: how to create a heatmap. So it takes off from a point where the user already has the matrix they want to plot. Perhaps a tutorial you're looking for would go over the R Data Frame and other R Objects. I'm certain there are good resources for this, like DataCamp.