Hi @jokergoo, Thanks to develop this greate tools, The matrix i put in Heatmap sparked the error like below, error: You should have at least two distinct break values in complexheatmap Why the error occurred when using the matrix to plot heatmap using complexheatmap R package. the original code showing below,

Heatmap(as.matrix(m))

The matrix displaying below,

Any advice would be appricated

Hi,

I looked at the help page for Heatmap, it seems only supports split on rows, and there is a gap parameter for it. Is it possible to split on columns as well?

A more detailed question is: when I do a supervised-clustering, I want to first split the columns (samples) into say 3 pre-defined subgroups first, and then do clustering within each subgroup for columns and do a k-means for all rows. Is it possible?

Now, I am manually arrange the data matrix into three distinct groups, and do a K means with the rows, and cluster_column=FALSE.

Thanks, Ming

Hi,

This is more like a general question. When making heatmap with too many rows, usually use EnrichedHeatmap with many (more than 10,000) genomic regions, the PDF size of the heatmap is very big (several MB). Computer becomes very slow when visualize it or when insert into powerpoint and Word. For other type of analysis, I usually use only top several hundred most variable rows to cluster.

I know it is more of a visualization than making any real quantitative comparisons. Our eyes probably can not differentiate these many pixels. How to reduce the size of the PDF?

Some time ago, I got a tip from this post

Now for my heatmap power tip of the day, if you will: use the "useRaster=TRUE" parameter in your heatmap.2() call. Excellent extension by R developers since 2.13. But for some reason the R developers explicitly turn it off for interactive session windows, so you'll only see it in an exported file. (Unless you have a custom image() function which doesn't disable it, I did this.) It also makes the exported file hugely smaller, especially for PDFs.

What it does is darn-near essential for nextgen coverage heatmaps -- it actually properly resamples the image as it down-sizes the image during export. Without useRaster=TRUE, image() creates a zillion tiny rectangles to represent the heatmap, all pieced together right next to each other. When the display is fewer pixels/points high than the number of rows of data, it discretizes the data -- that is, it uses integer values for the rectangles. In many cases, especially onscreen, many rectangles fully overlap others, randomly obscuring the real patterns, and often blunting your otherwise cool-looking signal.

useRaster=TRUE is only for heatmap.2 or internally image(). Is there a way to specify it in ComplexHeatmaps or how do you usually deal with this situation?

Thanks, Ming

Some of the logic within HeatmapAnnotation()'s system call check code breaks down when it is called within do.call(pheatmap, ...)

library(ComplexHeatmap)

mat <- matrix(rpois(30, 20), ncol=5)
rownames(mat) <- paste0("gene", 1:6)
colnames(mat) <- paste0("samp", 1:5)

annotation_col <- data.frame(score = 1:5,
                             row.names = colnames(mat))

# Direct call works
pheatmap(mat, annotation_col = annotation_col)

# indirect call with do.call
do.call(pheatmap, list(mat, annotation_col = annotation_col))
> Error in as.character(scl[[1]]) : 
    cannot coerce type 'closure' to vector of type 'character'

The error comes from this line, https://github.com/jokergoo/ComplexHeatmap/blob/a5cd974897746990d16843724d71822ccd771feb/R/HeatmapAnnotation-class.R#L161 and results from scl[[1]] being the function definition itself, rather than its symbolic name. Thus as.character() fails.

I'm not sure of the best solution here, but it may help that is.symbol(scl[[1]]) evaluates to TRUE for direct calls but FALSE for indirect calls through do.call.

ComplexHeatmap::Heatmap(matrix(c(0, 0, 1, 1), nrow=2))

gives

Error in valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,  :
  invalid 'xscale' in viewport

Hi,

I want to split the columns unevenly. I have 34 samples and want to split it to 8-26 in the oncoPrint. I tried to search the wiki, but I am unable to find the proper usage for that. It always gives me the error that "the number of columns should be equal to the ncol of matirx"

Also I am using, column_order and column)split both, so should I define a list of column orders since I am splitting the matrix?

You help is much appreciated.

Thanks, Rashesh

Hey, I was wondering how to apply my customized dendrogram to the heatmap. I first generated a heatmap with specified clustering method in Heatmap commend:

Heatmap(matrix_new, cluster_columns =T, cluster_rows=F, clustering_distance_columns = "pearson", clustering_method_columns = "ward.D")

Then, I customized the dendrogram using the following codes

hc <- hclust(as.dist(1-cor(t(sample.norm[,1:18]),method="pearson")),method="ward.D") dd <- as.dendrogram(hc) dd.reorder = reorder(dd, c(rep(10, 22),rep(9,27),rep(1,49)), agglo.FUN = mean)

When I plot the customized dendrogram, it did changed into the way I want. And I assigned the customized dendrogram to the heatmap I created at the first:

Heatmap(matrix_new, cluster_columns = dd.reorder, cluster_rows=F)

However, the dendrograms in two heatmaps did not change. I am not sure what went wrong, and come here for some help. Any advise?

Thanks, Stingo

Greetings!

I was wondering if it is possible to add a table along the height of the heatmap to depict multiple pieces of information about the column? For instance, I want to show the gene locus number in one column, the gene name in a second, and what it is identified as in a different organism in a third column. I have gone through the how to web pages for the ComplexHeatmap package, and I saw nothing. Is what I am suggesting possible for your package? If not, do you have any suggestions as to how I might be able to implement this?

Thank you very much for your time!

Hi jokergoo, I'm working on a new project and I make some complexheatmaps. However when I open the R project and I load the library {ComplexHeatmap}, I get these warnings:

Warning messages:
1: Not a validObject(): no slot of name "subsetable" for this object of class "HeatmapAnnotation" 
2: Not a validObject(): no slot of name "subsetable" for this object of class "SingleAnnotation" 
3: Not a validObject(): no slot of name "subsetable" for this object of class "AnnotationFunction" 
4: Not a validObject(): no slot of name "subsetable" for this object of class "HeatmapAnnotation" 
5: Not a validObject(): no slot of name "subsetable" for this object of class "SingleAnnotation" 
6: Not a validObject(): no slot of name "subsetable" for this object of class "AnnotationFunction" 

The problem appears only when I load the package inside this R project and only the first time I load it. In other R project I don't have it. Do you know why I have these warnings? I don't even understand what do they mean.

I have the latest version of R (4.1.3) and ComplexHeatmap (2.10.0).

Thank you for putting together and maintaining ComplexHeatmap. I just got started with the github version 2.9.3 (July 29, 2021) on R Version 4.0.2. Heatmap() runs without any issue for the first heatmap. But, on trying to repeat this with the same matrix, R freezes. This occurs both with RStudio and from R Console.

Here are some snippets from running devtools::session_info()

- Session info -----------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/New_York            
 date     2021-07-29 

 ComplexHeatmap * 2.9.3    2021-07-29 [1] Github (jokergoo/[email protected])

Thanks, Vishal

Hi,

When we use the parameter heatmap_legend_side to move the legends to the bottom draw(ht, heatmap_legend_side = "bottom"), it only moves the legends from the onconprint, but not for annatations to the bottom.

How can I do that? I would like to have all legends in the bottom. Thanks.

Hello!

Thanks for ComplexHeatmap!! I was wondering what's the best way to get something like B here (Alvisi G,et al. Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target. J Hepatol. 2022 Nov;77(5):1359-1372.):

I have a gene co-expression heatmap and I want to show selected genes in the areas of high correlation. Here is my attempt with anno_mark:

position <- which(rownames(mat)%in%genes)

row_an <- rowAnnotation(Genes = anno_mark(at = position,
                                           labels = rownames(mat)[position],
                                           labels_gp = gpar(fontsize = 6),
                                           link_width = unit(5, "mm"),
                                           padding = unit(1, "mm"),
                                           link_gp = gpar(lwd = 1),
                                          extend = unit(1, "mm")))

ht.3 <- Heatmap(mat, name = "Spearman correlation",
                column_names_gp = grid::gpar(fontsize = 0),
                row_names_gp = grid::gpar(fontsize = 0),
                right_annotation = row_an,
                heatmap_legend_param = list(legend_direction = "horizontal")) 
draw(ht.3, heatmap_legend_side = "bottom")

where genes are the selected genes I want to plot.

This is what I get:

The heatmap is a bit confusing. I tried to use anno_zoom or anno_textbox but would like to maintain the rows clustering and I would prefer not to split the rows.

Is it doable?

Thanks, Francesco

So I have been trying to troubleshoot this issue I have run into when generating publication quality grouped heatmaps.

I am attaching 3 heatmaps which are generated from three different matrices, but which are all generated in exactly the same way. The code to generate the heatmaps is also exactly the same ( it is one function iterated over the three matrices.)

However, for some reason I have yet to understand, they have strikingly different 'pixel' size. This is visible directly in the in-line RStudio image device... as well as after exporting at 1200 DPI PNG files.

Any ideas? I'm including the size of the data matrices for comparison:

Heatmap 1: 875 columns x 2119 rows

Heatmap 2: 674 columns x 1743 rows

Heatmap 3: 241 ccolumns x 1780 rows

ginfo:

anno209 <- rowAnnotation(
    log2fc1 = anno_numeric(ginfo$log2FC209 %>% nice_round(., digit=3), 
                           bg_gp = gpar(fill = ginfo$col209),
                           labels_gp = gpar(fontsize = letter_size),
                           bar_width = unit(1, "npc") - unit(2, "pt")), 
    annotation_name_rot = row_anno_rot,
    annotation_name_gp = gpar(fontsize = label_size, fontface = "bold"),
    width=unit(c(row_anno_width), "in"),
    annotation_name_offset = unit(c(row_anno_offset), "mm"),
    annotation_label = "log2FC 209_5 VS 313_1" 
  );

I intended to have log2FC barplot as a row annotation using anno_numeric, fill the bars that are significantly (padj209 <= 0.05) upregulated (log2FC209 > 0) red, significantly (padj209 <= 0.05) downregulated (log2FC209 < 0) green, not significant (padj209 > 0.05) white. Based on the criteria, I have the color ready as col209. Using the code above, I got bar annotation as below:

Basically, it failed to add the color appropriately. Do you know how to fix it?

Thank you very much, Wendy

Dear Jokergoo, Congratulations on developing and maintaining this fantastic package. Easily one of my favourite R packages overall.

I've recently stumbled across a frustrating error whilst trying to make an UpSet plot annotated with different intersect methods. For context, I've made this type of plot before (shown below), and in fact even recycled the code when trying to remake it this time. My problem is that I can make each UpSet plot (intersect, distinct, and union) separately fine (shown below), but when I tried to add them into the same plot I get the following error: "Error: Length of annotations differs. distict: 7, intersect: 11, union: 15" (notice also the little spelling mistake in "distict").

And here is my code

Sets <- list(
Abd.Fem   = vector1,
Glu.Fem    = vector2,
Abd.Man  = vector3,
Glu.Man   = vector4)
UPSets.intersect <- make_comb_mat(Sets, mode = "intersect", min_set_size = 0)
UPSets.intersect.distinct <- make_comb_mat(Sets, mode = "distinct", min_set_size = 0)
UPSets.intersect.union <- make_comb_mat(Sets, mode = "union", min_set_size = 0)
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
Sets.Upset.Plot <-
UpSet(t(UPSets.intersect.distinct[comb_degree(UPSets.intersect.distinct) > 0]),
      comb_order = order(-comb_size(UPSets.intersect.distinct[comb_degree(UPSets.intersect.distinct) > 0])),
      set_order = c("Abd.Fem","Glu.Fem","Abd.Man","Glu.Man"),
      pt_size = unit(5, "mm"),
      lwd = 3,
      bg_col = c("#f5e1e1","#f5e1e1","#e7f5fe","#e7f5fe"),
      right_annotation = rowAnnotation(
    "distict" = anno_barplot(comb_size(UPSets.intersect.distinct), 
        gp = gpar(fill = "black"), width = unit(1.5, "cm")), 
    "intersect" = anno_barplot(comb_size(UPSets.intersect), 
        gp = gpar(fill = "black"), width = unit(1.5, "cm")), 
    "union" = anno_barplot(comb_size(UPSets.intersect.union), 
        gp = gpar(fill = "black"), width = unit(1.5, "cm")), 
    gap = unit(2, "mm"), annotation_name_side = "bottom"))

Error: Length of annotations differs. distict: 7, intersect: 11, union: 15

Is it possible to plot these together, as last time, or does the data this time somehow make it impossible? I am using ComplexHeatmap version 2.15.1, downloaded from GitHub today. Your help is very much appreciated! Best wishes, Daniel

Hello, Thank you very much for this great package, I use it every time. I was looking to know if it would be possible to remove the white space between sample to get an oncoprint that looks like this ?

Thank you! Evan

Hello, I am trying to make a barplot annotation. The values are between -1 and 1 and I would like to make the filling color gradient like in heatmap using colorRamp2(c(-1, 0, 1), c("green", "white", "red")), but it didn't work If I specify in Signature = anno_barplot(sinfo %>% pull(Signature), height = unit(1.2, "cm"), gp = gpar(fill = colorRamp2(c(-1, 0, 1), c("green", "white", "red")))) Do you have any suggestions? The purpose is to color the following barplots in gradient.

Thank you very much!