Comments (4)
Thanks for your questions @josruirod ! Preliminary thoughts:
- Can you share an example of what you mean? I'm not sure I fully understand the desired behavior.
- With
add_row_clusters
there is currently no option to control the ordering within clusters. That seems like a useful feature. For now, there are lower level functions that allow you to control the ordering and clustering more finely. I'll try to make an example of that to share. - No methods for custom text annotations (other than the
add_col_labels
andadd_col_title
). Theadd_col_labels
type of method might be able to be adapted for this use case, although it wouldn't be straightforward (basic idea is that you can specify what columns to label (doesn't need to be all and what label you want to use, so you could just label one row per cluster).
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Thank for your clarifications.
- Forgive my poor explanation, I give some example now using "Indometh_patient_cor" dataset from the Vignette
iheatmap(Indometh_patient_cor,name = "Correlation",
scale = c("rows"), scale_method = c("center"))
This provides a heatmap where the values range to -0.03 to 0.029.
Using the same matrix with other typical heatmaps packages, like pheatmap, that scale changes.
pheatmap(Indometh_patient_cor, scale = c("row"))
I believe pheatmap scaling row-wise takes also into account sd, but what I find interesting is that by default provides a colorbar ranging from -1.5 to 1.5 value. And the fact that this can be changed using the breaks argument for example.
I wondered if in any way we can control the range of values in the colorbar with your function. It could be interesting for example to get the same range of positive or negative values or to force the same scale in different plots in order to compare them.
- Thanks for your insights about the last points. Regarding the ordering, I have indeed used other functions and then provided my desired order to the plot. I'm sure an example is something nice to add, it would be useful to the ones who did not think about it at first.
Regarding the custom text annotations, as far as I'm concerned there are no equivalent functions to text() or mtext() to use in interactive plots like these. A similar method specifying custom text and coordinates or location would be great to fine tuning the annotation, but of course it's not a big problem.
Thank you so much for answering and for your feedback!
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Thanks for the clarification about the scaling!
Regarding the scale issue, "center" just subtracts the mean, while "standardize" subtracts the mean and divides by the standard deviation. The "standardize" option will give results comparable to pheatmap scaling method. I realize this wasn't very clear in documentation and have updated the man page for iheatmap
function.
For more control over min/max of range, using the lower level main_heatmap
function gives more options -- the zmin
and zmax
arguments specify the max/min of the colorbar/scale. You can also pass those arguments to iheatmap
as all extra arguments to iheatmap
get passed along to main_heatmap
. Currently no options to fine tune the exact breaks desired, but I agree that would be a nice additional feature.
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Thank you so much for your insights, all clear now. Regards
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Related Issues (20)
- textangle messes-up the row or column labels HOT 1
- layout of colorbars of annotations
- Reverse dependency checks fail with `ggdendro` HOT 5
- Adding empty annotation causes an error HOT 2
- Single row heatmap does not show HOT 2
- Column annotation label disappeared HOT 10
- Scale the main_heatmap
- Add extra markings to specific cells
- Bug: error causes heatmap to disappear if it tries to re-plot after a plotly plot is rendered HOT 1
- iheatmapr in shiny is not responsive HOT 1
- renderIheatmap breaks when used with shiny::req HOT 3
- Using multiple colors for axis ticks HOT 2
- Add animation/slider function
- Decorate heatmap body
- [FEATURE REQUEST] Use with Chart studio HOT 1
- How to change the row order of the heatmap from Alabama to Wyoming ? [Question] HOT 4
- Buffer and size dendrogram argument to add_*_clustering
- iheatmapr doesn't work when on the same HTML page as a standard plotly widget HOT 1
- Resize width and height of html file using saveWidget or save_iheatmap
- CRAN deprecation HOT 3
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