I was having some trouble following along because I kept getting an error "Unused argument" when trying to run " row_hclust_side = ..." and then I changed it to "row_dend_side" and "row_dend_width" and now it works. I guess the arguments names have changed in newest versions. I am using R 4.0 and latest ComplexHeatmap version downloaded today :)
Glad to hear that! There's more over on the OMGenomics channel where I'm posting new videos these days, so make sure to check that out when you get a chance!
hey ，my friend! Have you met this error "annotations should have names" When i run the last list of code "Heatmap(my_matrix, cluster_columns=FALSE, row_names_side = "left", row_dend_side = "left", row_names_gp=gpar(cex=fontsize), row_dend_width = unit(3, "cm"), clustering_distance_rows ="maximum", clustering_method_rows = "ward.D", km=2, # number of clusters you want bottom_annotation = HeatmapAnnotation(chromosome_info,col = list(chrom=chromosome.colors),show_legend=FALSE) )" , it always tell me "annotations should have names" .
Hi Maria Nattestad, I was trying from last 2 days to do the Lesson-08/copy_number for r plots. But unfortunately i was not able to load the data. I got stuck their. here i am posting the command line > filename
Hey! very impressive video and easy to understand. I found it very difficult to use. Can you please tell me how can i use ComplexHeatmap package in R. I have downloaded from the bioconductor bt can't found in the library of R. Please help me asap. Thank you.
It's in the script I'm showing in the video at 1:41. If anything there is outdated, check the Bioconductor website for the latest installation information: www.bioconductor.org/install/
Can you please tell me how can I normalize my gene expression dataset that I have downloaded from the GEO database. Please respond me asap. I need detailed information about the script and packages used for the normalization.
"annotations should have names" When i run the last list of code "Heatmap(my_matrix, cluster_columns=FALSE, row_names_side = "left", row_dend_side = "left", row_names_gp=gpar(cex=fontsize), row_dend_width = unit(3, "cm"), clustering_distance_rows ="maximum", clustering_method_rows = "ward.D", km=2, # number of clusters you want bottom_annotation = HeatmapAnnotation(chromosome_info,col = list(chrom=chromosome.colors),show_legend=FALSE) )" , it always tell me "annotations should have names" . Does anyone else also has the error????
Hi Thank you for the nice video: I just face an error at the very end - Error: annotations should have names. Could you please give a look to the following? What is wrong with this? Heatmap(my_matrix, + cluster_columns=FALSE, + row_names_side = "left", + row_dend_side = "left", + row_names_gp=gpar(cex=fontsize), + row_dend_width = unit(3, "cm"), + clustering_distance_rows ="maximum", + clustering_method_rows = "ward.D", + km=2, # number of clusters you want + bottom_annotation = HeatmapAnnotation(chromosome_info,col = list(chrom=chromosome.colors),show_legend=FALSE) + ) Error: annotations should have names.
HI Maria, thank you so much for your videos, it is so helpful for me, just I have a small question concern the last part of this video Heatmap(my_matrix, cluster_columns=FALSE, row_names_side = "left", row_dend_side = "left", row_names_gp=gpar(cex=fontsize), row_dend_width = unit(3, "cm"), clustering_distance_rows ="maximum", clustering_method_rows = "ward.D", km=2, # number of clusters you want bottom_annotation =HeatmapAnnotation(chromosome_info,names,col=list(chrom=chromosome.colors), show_legend=FALSE) ) I got that as a message Error: annotations should have names. someone can help with that Thanks again
Hi, I have now figured out the code: Heatmap(my_matrix, cluster_columns=FALSE, row_names_side = "left", row_dend_side = "left", row_names_gp=gpar(cex=fontsize), row_dend_width = unit(3, "cm"), clustering_distance_rows ="maximum", clustering_method_rows = "ward.D", km=2, # number of clusters you want bottom_annotation = HeatmapAnnotation(df = chromosome_info, col = list(chrom=chromosome.colors), show_legend=FALSE)) You have to assign chromosome_info as dataframe! Best, Teresa
I was having some trouble following along because I kept getting an error "Unused argument" when trying to run " row_hclust_side = ..." and then I changed it to "row_dend_side" and "row_dend_width" and now it works. I guess the arguments names have changed in newest versions. I am using R 4.0 and latest ComplexHeatmap version downloaded today :)
Thanks for posting after you figured it out! I'm pinning this to the top and adding a note to the description :)
@@MariaNattestad Of course! Thank you for the tutorial :)
@@MariaNattestad Thank you thank you thank you, you're a bless!!
I recommended this channel to all my classmates at GMU, B.S. Bioinformatics
Thanks for the great tutorial.
Hey great video! I’m doing my postdoc and I’m trying to learn bioinformatics and your videos are so helpful! Thanks for sharing your knowledge!
Thank you so much for actually showing the data structure at the beginning.
This may be old and some of the code my be updated (regarding clustering), but this is easily the best heatmap tutorial I have found anywhere.
Thanks! :D
Thank you for your series. Lots of good examples and this is a great way to get comfortable with ggplot.
Glad to hear that! There's more over on the OMGenomics channel where I'm posting new videos these days, so make sure to check that out when you get a chance!
its really help full for me to understand how to draw a heat map in R thank you Maria Nattestad
How do you set the heatmap to use Bray-Curtis method and do you have to scale your data before plotting?
very clear explanation! nice video! I got one question: which distance method would you use with log2FC or raw(but scaled) values? many thanks
Just finished the 8 lessons in 2021 (am late to the party, i know haha) and feel pretty confident about tackling my own projects! Thanks so much!!
hey ，my friend! Have you met this error
"annotations should have names"
When i run the last list of code
"Heatmap(my_matrix,
cluster_columns=FALSE,
row_names_side = "left",
row_dend_side = "left",
row_names_gp=gpar(cex=fontsize),
row_dend_width = unit(3, "cm"),
clustering_distance_rows ="maximum",
clustering_method_rows = "ward.D",
km=2, # number of clusters you want
bottom_annotation = HeatmapAnnotation(chromosome_info,col = list(chrom=chromosome.colors),show_legend=FALSE)
)"
, it always tell me "annotations should have names" .
I really liked this video. It is so easy to follow with a clear motive.
Thank you so much Maria, your tutorial was very straight forward and easy to understand.
Thank you for your series, your tutorial was very straight forward and easy to understand.
Anyone know if "Complexheatmap" are going to incorporate "Bray-Curtis" distance calculations soon??
Thanks for all the videos you've created
Great tutorial Maria, simple and easy. Thanks
I am unable to download the data. Could you please help me to download it.
Thanks
How to change the colourscheme?
Please make a video on whole exome data Visualization
This is immensely useful. Thank you so much.
Hi Maria, thank you for series. i want to know how to get these Code, data, and video? Thank you!
the link is in the description: marianattestad.com/blog
Hi Maria Nattestad, I was trying from last 2 days to do the Lesson-08/copy_number for r plots. But unfortunately i was not able to load the data. I got stuck their. here i am posting the command line
> filename
Are you in the correct working directory?
Hey! very impressive video and easy to understand. I found it very difficult to use. Can you please tell me how can i use ComplexHeatmap package in R. I have downloaded from the bioconductor bt can't found in the library of R. Please help me asap. Thank you.
It's in the script I'm showing in the video at 1:41. If anything there is outdated, check the Bioconductor website for the latest installation information: www.bioconductor.org/install/
Can you please tell me how can I normalize my gene expression dataset that I have downloaded from the GEO database. Please respond me asap. I need detailed information about the script and packages used for the normalization.
Please help me. 🙏
Nice work Maria, Thank you.
You are so good. Thank you Maria!!!
"annotations should have names"
When i run the last list of code
"Heatmap(my_matrix,
cluster_columns=FALSE,
row_names_side = "left",
row_dend_side = "left",
row_names_gp=gpar(cex=fontsize),
row_dend_width = unit(3, "cm"),
clustering_distance_rows ="maximum",
clustering_method_rows = "ward.D",
km=2, # number of clusters you want
bottom_annotation = HeatmapAnnotation(chromosome_info,col = list(chrom=chromosome.colors),show_legend=FALSE)
)"
, it always tell me "annotations should have names" . Does anyone else also has the error????
See updates in description.
@@MariaNattestad Thanks, i will try to solve it. Looking forward for more courses from you . 🥰
Thank you so much Maria!
excelent lecture! Thanks!
Hi
Thank you for the nice video:
I just face an error at the very end - Error: annotations should have names.
Could you please give a look to the following? What is wrong with this?
Heatmap(my_matrix,
+ cluster_columns=FALSE,
+ row_names_side = "left",
+ row_dend_side = "left",
+ row_names_gp=gpar(cex=fontsize),
+ row_dend_width = unit(3, "cm"),
+ clustering_distance_rows ="maximum",
+ clustering_method_rows = "ward.D",
+ km=2, # number of clusters you want
+ bottom_annotation = HeatmapAnnotation(chromosome_info,col = list(chrom=chromosome.colors),show_legend=FALSE)
+ )
Error: annotations should have names.
I am getting the same error - any luck with it ?
I am getting the same error, i cannot get around it at all...
Thanks for all the lessons! :)
Thank you Maria
Very helpful . Thanks
HI Maria, thank you so much for your videos, it is so helpful for me, just I have a small question concern the last part of this video
Heatmap(my_matrix,
cluster_columns=FALSE,
row_names_side = "left",
row_dend_side = "left",
row_names_gp=gpar(cex=fontsize),
row_dend_width = unit(3, "cm"),
clustering_distance_rows ="maximum",
clustering_method_rows = "ward.D",
km=2, # number of clusters you want
bottom_annotation =HeatmapAnnotation(chromosome_info,names,col=list(chrom=chromosome.colors), show_legend=FALSE)
)
I got that as a message
Error: annotations should have names.
someone can help with that
Thanks again
I face the same error! Have you already figures out the problem?
I would really appreciate your help!! =)
Hi, I have now figured out the code:
Heatmap(my_matrix,
cluster_columns=FALSE,
row_names_side = "left",
row_dend_side = "left",
row_names_gp=gpar(cex=fontsize),
row_dend_width = unit(3, "cm"),
clustering_distance_rows ="maximum",
clustering_method_rows = "ward.D",
km=2, # number of clusters you want
bottom_annotation = HeatmapAnnotation(df = chromosome_info, col = list(chrom=chromosome.colors), show_legend=FALSE))
You have to assign chromosome_info as dataframe!
Best,
Teresa
@@Teresa-xt8oi no ... that gets an error too "Error: number of observations in bottom anntotion should be as same as
ncol of the matrix."
@@Teresa-xt8oi Thank you for this solution, I had the same error.
Will see and comment
thx