boxplots in baseline positive

[benkeser]

@yiwenlu @KenLi93

Currently, plots with label boxplots_Delta57overB_trt_vaccine_x_cc_BaselinePos_ are not being generated as part of the Makefile, but they are included in report.Rmd. Should these plots be included in the report? If so, how can the code be modified to generate these plots?

[benkeser]

Here is the chunk of code in report.Rmd in question:

```{r, fig.cap = "(Mock data) Boxplots of D29 Ab markers: baseline positive vaccine arm by cases and non-cases"}

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Day29_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Day57_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Delta29overB_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Delta57overB_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

[KenLi93]

Hi David,

Thank you for spotting this! Is this the cor_graphical or immuno_graphical folder?

Best regards, Kendrick

On Tue, Feb 23, 2021, 8:20 AM David Benkeser notifications@github.com wrote:

Here is the chunk of code in report.Rmd in question:

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Day29_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Day57_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Delta29overB_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

    knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Delta57overB_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

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[benkeser]

cor_graphical

---

From: KenLi93 notifications@github.com Sent: Tuesday, February 23, 2021 11:28 AM To: CoVPN/correlates_reporting correlates_reporting@noreply.github.com Cc: Benkeser, David benkeser@emory.edu; Author author@noreply.github.com Subject: [External] Re: [CoVPN/correlates_reporting] boxplots in baseline positive (#52)

Hi David,

Thank you for spotting this! Is this the cor_graphical or immuno_graphical folder?

Best regards, Kendrick

On Tue, Feb 23, 2021, 8:20 AM David Benkeser notifications@github.com wrote:

Here is the chunk of code in report.Rmd in question:

knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Day29_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Day57_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Delta29overB_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

knitr::include_graphics(here::here("cor_graphical", "figs", paste0("boxplots_Delta57overB_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

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[KenLi93]

Hi David,

It seems the code in my local make file is somehow not integrated into the master. Could you please add the following lines to cor_graphical/make? Thanks! I have checked the code locally and they worked on my pc.

Best regards, Kendrick

all: cor_boxplots cor_wrcdf

boxplots by case and non-case

cor_boxplots: code/cor_data_preprocess.R \ plot_data params Rscript code/CoR_assay_graphics.R

weighted rcdf:

cor_wrcdf: code/cor_data_preprocess.R \ plot_data params Rscript code/CoR_wrcdf_with_VE_lines.R

plot_data : relabel and clean data sets for plotting

creates clean_data/long_twophase_data.rds and clean_data/twophase_data.rds

plot_data: code/cor_data_preprocess.R params Rscript code/cor_data_preprocess.R

parameters that may vary across runs

params: code/params.R

clean : delete contents of data_clean/ and figs/

clean: rm -f data_clean/.rds rm -f figs/.png rm -f Rplots.pdf

On Tue, Feb 23, 2021 at 8:43 AM David Benkeser notifications@github.com wrote:

cor_graphical

---

From: KenLi93 notifications@github.com Sent: Tuesday, February 23, 2021 11:28 AM To: CoVPN/correlates_reporting correlates_reporting@noreply.github.com Cc: Benkeser, David benkeser@emory.edu; Author < author@noreply.github.com> Subject: [External] Re: [CoVPN/correlates_reporting] boxplots in baseline positive (#52)

Hi David,

Thank you for spotting this! Is this the cor_graphical or immuno_graphical folder?

Best regards, Kendrick

On Tue, Feb 23, 2021, 8:20 AM David Benkeser notifications@github.com wrote:

Here is the chunk of code in report.Rmd in question:

positive vaccine arm by cases and non-cases"}

knitr::include_graphics(here::here("cor_graphical", "figs",
paste0("boxplots_Day29_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

positive vaccine arm by cases and non-cases"}

knitr::include_graphics(here::here("cor_graphical", "figs",
paste0("boxplots_Day57_trt_vaccine_x_cc_BaselinePos_", study_name, ".png")))

markers: baseline positive vaccine arm by cases and non-cases"}

knitr::include_graphics(here::here("cor_graphical", "figs",
paste0("boxplots_Delta29overB_trt_vaccine_x_cc_BaselinePos_", study_name,
".png")))

markers: baseline negative vaccine arm by cases and non-cases"}

knitr::include_graphics(here::here("cor_graphical", "figs",
paste0("boxplots_Delta57overB_trt_vaccine_x_cc_BaselinePos_", study_name,
".png")))

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If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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-- Kendrick Li

Department of Biostatistics

University of Washington

He/Him/His

[benkeser]

I've included those already in the Makefile and the referenced figures are not produced. Please check the .R scripts.

[KenLi93]

Hi David,

After checking the R scripts and the past emails from Peter, I realized all the plots for baseline positive subjects were removed from the R code but haven't been removed from report.rmd. I will make the changes and send in a new pull request.

Sorry for the confusion!

Best regards, Kendrick

On Tue, Feb 23, 2021 at 9:55 AM David Benkeser notifications@github.com wrote:

I've included those already in the Makefile and the referenced figures are not produced. Please check the .R scripts.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/CoVPN/correlates_reporting/issues/52#issuecomment-784387954, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJRJJJUUXKGWQJHXW7SKGRDTAPTW3ANCNFSM4YCYR7FA .

-- Kendrick Li

Department of Biostatistics

University of Washington

He/Him/His