add citation

Author: qingjian1991

.gitignore

@@ -13,5 +13,4 @@ documents/MPTevol_cache
 documents/rsconnect
 documents/MPTevol_files
 documents/MPTevol.html
-vignettes
 Test.R

README.Rmd

@@ -18,17 +18,19 @@ knitr::opts_chunk$set(
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-The goal of MPTevol is to provide a practical computation framework for dissecting the
-evolution of multiple primary tumors (MPT), reducing analysis
-complexity with modular design.
+Multiple primary tumors (MPT) is a special and rare cancer type, defined as more than two primary tumors presenting at the diagnosis in a single patient. The molecular characteristics and tumorigenesis of MPT remain unclear due to insufficient approaches.
+ 
+Here, we present `MPTevol`, a practical computational framework for comprehensively exploring the MPT from **multiregional sequencing (MRS)** experiments. `MPTevol` facilitates comparison genomic profiles across multiple primary tumor samples, detection of clonal evolutionary history and metastatic routines in MPT, and quantification of metastatic history. This package incorporates multiple cancer evolution analyses, for a one-stop solution of MPT analysis.The goal of MPTevol is to provide a practical computation framework for dissecting the evolution of multiple primary tumors (MPT), reducing analysis complexity with modular design.
 
-**Package Overview**:
+## Package Overview
 
 ![](man/figures/MPTevol.jpg)
 
+## Citations
+
 If you are using the MPTevol in academic research, please cite our paper:
 
-***Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple primary tumors and multiple metastases with MPTevol.***
+**Chen, Q., Wu, Q.-N., Rong, Y.-M., Wang, S., Zuo, Z., Bai, L., . . . Zhao, Q. (2022). Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol. Briefings in Bioinformatics. doi:10.1093/bib/bbac175**
 
 ## Installation
 

README.md

@@ -6,20 +6,36 @@
 <!-- badges: start -->
 <!-- badges: end -->
 
-The goal of MPTevol is to provide a practical computation framework for
-dissecting the evolution of multiple primary tumors (MPT), reducing
-analysis complexity with modular design.
-
-**Package Overview**:
+Multiple primary tumors (MPT) is a special and rare cancer type, defined
+as more than two primary tumors presenting at the diagnosis in a single
+patient. The molecular characteristics and tumorigenesis of MPT remain
+unclear due to insufficient approaches.
+
+Here, we present `MPTevol`, a practical computational framework for
+comprehensively exploring the MPT from **multiregional sequencing
+(MRS)** experiments. `MPTevol` facilitates comparison genomic profiles
+across multiple primary tumor samples, detection of clonal evolutionary
+history and metastatic routines in MPT, and quantification of metastatic
+history. This package incorporates multiple cancer evolution analyses,
+for a one-stop solution of MPT analysis.The goal of MPTevol is to
+provide a practical computation framework for dissecting the evolution
+of multiple primary tumors (MPT), reducing analysis complexity with
+modular design.
+
+## Package Overview
 
 ![](man/figures/MPTevol.jpg)
 
+## Citations
+
 If you are using the MPTevol in academic research, please cite our
 paper:
 
-***Deciphering clonal dynamics and metastatic routines in a rare patient
-of synchronous triple primary tumors and multiple metastases with
-MPTevol.***
+**Chen, Q., Wu, Q.-N., Rong, Y.-M., Wang, S., Zuo, Z., Bai, L., . . .
+Zhao, Q. (2022). Deciphering clonal dynamics and metastatic routines in
+a rare patient of synchronous triple-primary tumors and multiple
+metastases with MPTevol. Briefings in Bioinformatics.
+<doi:10.1093/bib/bbac175>**
 
 ## Installation
 

Test.R

@@ -5,9 +5,6 @@ use_gpl_license(version = 3, include_future = TRUE)
 
 library(usethis)
 
-
-add_
-
 #add packages.
 use_package("tidyverse", type = "depends")
 

documents/MPTevol.Rmd

@@ -106,7 +106,7 @@ remotes::install_github("qingjian1991/MPTevol")
 
 If you are using `MPTevol` in academic research, please cite the following paper:
 
-***Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple primary tumors and multiple metastases with MPTevol***
+***Chen, Q., Wu, Q.-N., Rong, Y.-M., Wang, S., Zuo, Z., Bai, L., . . . Zhao, Q. (2022). Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol. Briefings in Bioinformatics. doi:10.1093/bib/bbac175***
 
 
 ## 2. Input data format
@@ -434,7 +434,9 @@ On the other hand,selective pressure can be estimated simply by the ratio of dri
 
 ```{r message=FALSE, eval=TRUE}
 prop <- calPropDriver(maf, patient.id = "BRCA", class = "SP", driverGene = driverGene)
-kaks$BRCA$plot + ggpubr::theme_pubr()
+cowplot::plot_grid(kaks$BRCA$plot + ggpubr::theme_pubr(),
+                   prop$BRCA$plot + ggpubr::theme_pubr()
+                   )
 ```
 
 The mutations in `BRCA` were divided into `Public`(shared by all sampling site), `Shared`(shared by two or more samples but not all sampling site), and `Private`(Private in one sampling site). The `Public` mutations were under positive selection (`Dn/Ds >=1` and `The prop of driver mutations is high` ), coherent with the expectation that the ancestral mutations might contribute to cancer development. 

vignettes/.gitignore

@@ -0,0 +1,4 @@
+*.html
+*.R
+rsconnect
+MPTevol_cache