Annotation Legends of col_side_colors disappear after applying clustering to both column and row

[JrTai]

No description provided.

[alanocallaghan]

Can you be more specific?

[JrTai]

The annotation legend generated by col_side_colors disappear after applying clustering to both column and row data.

Before applying clustering:

After applying clustering to both column and row:

Many Thanks for helping with this problem!

Best,
Tai

[alanocallaghan]

Thanks, im busy for the next few days but will try to have a look after that On 22 Jan 2018 6:23 pm, Jr-Han Tai <notifications@github.com> wrote: The annotation legend generated by col_side_colors disappear after applying clustering to both column and row data. Before applying clustering: [before clustering]<https://user-images.githubusercontent.com/8951652/35236973-cd01e5d0-ff6e-11e7-8cb9-86fa6069eeee.jpg> After applying clustering to both column and row: [after clustering]<https://user-images.githubusercontent.com/8951652/35236997-e456ca20-ff6e-11e7-8c0f-ca8977778cb3.jpg> — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#144 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AKR8KOi--Ozs0t6-Q3krvoC4UFjYlAosks5tNNIngaJpZM4RoaJf>.

[JrTai]

Thanks a lot for your time! :)

[alanocallaghan]

For the time being, you can set plot_method = "plotly" in your call to heatmaply, which should show a colour legend for the side colours.

[JrTai]

Hi Alanocallaghan,

Thanks a lot for the suggestion. I have tried setting plot_method = "plotly" in my heatmaply. It shows the annotation legend but seems some of the text is overlapped.

Before clustering (some text has little overlapped):

After clustering to both column and row (it shows the legend for the proper position):

After clustering to both column and row with a longer categories list (the text is totally overlapped):

[alanocallaghan]

How many unique values are in the column annotation?

[JrTai]

For the last example above, I have 49 unique values are in the column annotation.

[alanocallaghan]

I can't replicate the problem, could you post an example?

[JrTai]

I have tried this test code in Rstudio

library(gplots)
library(heatmaply)

df<- data.frame(replicate(49,sample(0:1,1000,rep=TRUE)))

annotation_df <- colnames(df)

heatmaply(df,
          fontsize_row = 7,
          fontsize_col = 7,

          plot_method = "plotly",

          col_side_colors = annotation_df,
          hide_colorbar = TRUE,

          dendrogram = "both"
          )

The small viewer shows the annotation text overlapped (49 unique values are in the column annotation ):

If I zoom the viewer to a bigger window, the annotation text shows better:

I have tried 70 unique values in the column annotation, even in the bigger window, the text is overlapped:

I think the position of annotation legend text showing depends on the size of heatmap window. There's also an upper limit for the annotation legend to show the text in the bigger zoom window.

I previously show the column annotation legend, the heatmap, in a quite small window. That why even 49 unique values cannot be displayed properly.

[alanocallaghan]

Cheers, I understand where the issue is coming from now but I haven't figured out a fix just yet

[alanocallaghan]

I'll deal with this in #141

[yikeshu0611]

Why always "col_side_colors" exists beside that！ Sometimes it seems not good.