I can't get the right png image

[zshu-alt]

I used the plot_zygosity_and_events.R file in version 1.0 to show that the object could not be found. I replaced this file with the file in version 0.9, which can produce a png image, but the image does not seem to be right, what is the problem? The log says I've run it successfully, only the image is bad

[findingdan]

It's been a while since i looked at this code and will need to revisit it. One thing that seems a bit unusual is the MI and B in the key

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On Mon, Oct 24, 2022 at 2:57 AM zshu-alt ***@***.***> wrote: I used the plot_zygosity_and_events.R file in version 1.0 to show that the object could not be found. I replaced this file with the file in version 0.9, which can produce a png image, but the image does not seem to be right, what is the problem? The log says I've run it successfully, only the image is bad [image: child exome sorted homREFed events_plot] <https://user-images.githubusercontent.com/83994276/197465845-0322f7fc-7459-4af2-8700-215193949653.png> — Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAXAWYBUW76BQSSZ265BS6LWEYXPLANCNFSM6AAAAAARMVSECU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[zshu-alt]

Thank you for your reply. I was looking at the 0.9 version of plot_zygosity_and_events.R and found that there might be a problem with the plot_sex<-commandArgs(trailingOnly=TRUE)[[4]] input. In the log file, I found:

Running R

$VAR1 = 'UPD/bin/R';

$VAR2 = '--slave -f';

$VAR3 = 'scripts';

$VAR4 = '/plot_zygosity_and_events.R --args';

$VAR5 = 'version_1. 0 / output_dir/child. Exome. Sorted. HomREFed. Events_list';

$VAR6 = 'version_1. 0 / sample_data/child. Exome. Sorted. HomREFed. VCF. Gz';

$VAR7 = 'version_1. 0 / output_dir';

$VAR8 = 'FALSE';

$VAR9 = 'FALSE';

UPDio finished successfully

$VAR8 = 'FALSE'; Will this result in no input plot_sex, what is this plot_sex file? Am I missing something?

[LET19]

@zshu-alt I got the same png result as you. And I found another message while runing this script:
"Loading required package: quantreg
Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

backsolve

Loading required package: grid

Attaching package: ‘quantsmooth’

The following objects are masked by ‘.GlobalEnv’:

characterCHR, numericCHR

"
seems like some functions with name conflicts?

[andrewdg98]

Hi, I'm having the same problem of @zshu-alt t (when I run the program it generates the same .png) and I also get the exact same message of @LET19. Did someone of you find a solution?
@findingdan is it correct to use the plot_zygosity_and_events.R file from version 0.9 as @zshu-alt suggested?