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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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why is there an error when drawing the result file? #591

Open zhongguozhiwang opened 1 year ago

zhongguozhiwang commented 1 year ago 
infercnv_obj = CreateInfercnvObject(raw_counts_matrix = counts,
                                        annotations_file = anno,
                                       delim="\t",
                                      gene_order_file = gene_order,
                                       min_max_counts_per_cell = c(100, +Inf),
                                     ref_group_names = c("Fibro", "endo"))

infercnv_obj = infercnv::run(infercnv_obj,
                                 cutoff = 0.1,
                                 out_dir = "result/", 
                                 cluster_by_groups = FALSE,
                                 HMM = FALSE,
                                 denoise = FALSE,
                                 num_threads = 8)

infercnv::plot_cnv(infercnv_obj,
                    plot_chr_scale = T,
                    output_filename = "better_plot",output_format = "pdf",
                    custom_color_pal =  color.palette(c("#8DD3C7","white","#BC80BD"), c(2, 2)))

INFO [2023-08-25 20:19:52] ::plot_cnv:Start INFO [2023-08-25 20:19:52] ::plot_cnv:Current data dimensions (r,c)=9400,8897 Total=83707578.1686258 Min=0.805765388786346 Max=4.9614932171772. INFO [2023-08-25 20:19:53] ::plot_cnv:Depending on the size of the matrix this may take a moment. INFO [2023-08-25 20:19:54] plot_cnv(): auto thresholding at: (0.900934 , 1.100879) INFO [2023-08-25 20:19:55] plot_cnv_observation:Start INFO [2023-08-25 20:19:55] Observation data size: Cells= 8513 Genes= 9400 ERROR [2023-08-25 20:19:55] Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error

zhongguozhiwang commented 1 year ago

The bottom half of the image is black and it is not known why this is the case. infercnv

sjasws commented 2 months ago

@zhongguozhiwang Did you solve the problem?

brianjohnhaas commented 2 months ago

Hi,

Try experimenting with the different hclust_methods:

-

'infercnv::run(hclust_method='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best.

On Fri, Jul 5, 2024 at 8:24 AM sjasws @.***> wrote:

@zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem?

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 2 months ago

Here's the list of options: ("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid")

On Sat, Jul 6, 2024 at 8:19 AM Brian Haas @.***> wrote:

Hi,

Try experimenting with the different hclust_methods:

-

'infercnv::run(hclust_method='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best.

On Fri, Jul 5, 2024 at 8:24 AM sjasws @.***> wrote:

@zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem?

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

sjasws commented 2 months ago

Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclust_method='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error.

I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem?

brianjohnhaas commented 2 months ago

I don't think so. We don't have anyone working on the project at the moment, and I haven't touched the codebase in years now - plus don't have time to support it, unfortunately. Tis the situation.

On Sat, Jul 6, 2024 at 8:32 AM sjasws @.***> wrote:

Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclustmethod='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … <#m-5484367672227859767_> On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 (comment) https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error.

I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem?

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2211756983, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM . You are receiving this because you commented.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

sjasws commented 2 months ago

I don't think so. We don't have anyone working on the project at the moment, and I haven't touched the codebase in years now - plus don't have time to support it, unfortunately. Tis the situation. … On Sat, Jul 6, 2024 at 8:32 AM sjasws @.> wrote: Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclustmethod='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … <#m-5484367672227859767_> On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 (comment) <#591 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error. I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem? — Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM . You are receiving this because you commented.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

In that case, I'll have to use infercnv's auto-generated figures. In any case, thank you very much to your team for providing such an excellent tool, which has helped me to infer tumor cells and their subclones.

brianjohnhaas commented 2 months ago

Great! I'm hoping we'll be back on track with supporting it again in the not too distant future.

On Sat, Jul 6, 2024 at 8:51 AM sjasws @.***> wrote:

I don't think so. We don't have anyone working on the project at the moment, and I haven't touched the codebase in years now - plus don't have time to support it, unfortunately. Tis the situation. … <#m7995038566241453533> On Sat, Jul 6, 2024 at 8:32 AM sjasws @.*> wrote: Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclustmethod='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … <#m-5484367672227859767_> On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 https://github.com/broadinstitute/infercnv/issues/591 (comment) <#591 (comment) https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas http://broad.mit.edu/~bhaas Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error. I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem? — Reply to this email directly, view it on GitHub <#591 (comment) https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2211756983>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM . You are receiving this because you commented.Message ID: @.***> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

In that case, I'll have to use infercnv's auto-generated figures. In any case, thank you very much to your team for providing such an excellent tool, which has helped me to infer tumor cells and their subclones.

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2211761255, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX74BAPCQLLPGJQUWETZK7R6RAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG43DCMRVGU . You are receiving this because you commented.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas