# app.R 代码
library(shiny)
ui <- fluidPage(
titlePanel("Manhattan plot"),
sidebarLayout(
sidebarPanel(
checkboxGroupInput("traits",label = h6("Choose traits"),choices = list("ANG_BTM"=4,
"ANG_TOP"=5,
"AREA"=6,
"AVG_DEN"=7,
"RTP_COUNT"=8,
"SKL_WIDTH"=9,
"WIDTH_MAX"=10,
"WIDTH_MED"=11),selected =4 ),
radioButtons("radio", label = h6("Choose manhattan plot type"),
choices = list("Horizontal version" = "m", "Circle version" = "c"),
selected = "c"),
sliderInput("slider1", label = h6("Threshold value"), min = 1e-6,
max = 1e-4,value = 1e-5),
helpText("Please note that because of the huge raw data,image plot and computation are slow.Please be patient.
After the download button is clicked, the image will be drawn. Please wait patiently and do not click multiple times.
Due to the computing power limitations of the site, the downloaded images are limited as 500 * 500 pixels.")
),
# Show a plot of the generated distribution
mainPanel(
tabsetPanel(type = "tabs",
tabPanel("plot",plotOutput("plot"))
)
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output) {
library(CMplot)
data<-read.table("datanew.txt",header = T)
output$plot <- renderPlot({
c_v<-c()
for (i in input$traits) {
c_v<-c(c_v,as.numeric(i))
}
datanew<<-data[,c(1:3,c_v)]
CMplot(datanew,type="p",plot.type=input$radio,r=0.4,chr.labels=paste("Chr",c(1:10),sep=""),
threshold=c(input$slider1),cir.chr.h=1.5,amplify=TRUE,
threshold.lty=c(1),threshold.col=c("red"),
signal.line=1,signal.col=c("red"),
chr.den.col=c("darkgreen","yellow","red"),
bin.size=1e6,outward=FALSE,file="jpg",
memo="",dpi=300,file.output=F,verbose=TRUE,width=1000,height=1000)
})
}
# Run the application
shinyApp(ui = ui, server = server)
最近考试超多的好嘛，卷起来了，但又没完全卷。今天看了篇分子生物学的文章，觉得还挺有趣的，按自己的思路便写写看。文章为2020年的nature plants，题为Transfer cells mediate nitrate uptake to control root nodule symbiosis（具体见参考文献文献）
摘要
根瘤共生为植物提供了固氮的能力，从而提高作物产量。环境硝酸盐水平影响着根系结瘤和固氮，但是豆科植物调节硝酸盐吸收以调节根瘤共生的机制仍不清楚。通过鉴定苜蓿NPF家族的一个成员NPF7.6，观察到NPF7.6在根瘤维管组织中特异性表达，且定位于根瘤转移细胞的质膜上，在那里NPF7.6起到高亲和硝酸盐转运体的作用。进一步通过构建NPF7.6的突变体，使得突变体在根瘤维管组织发育异常，且表现出硝酸盐吸收减少、一氧化氮稳态紊乱和固氮酶活性减弱，基于此提出了NPF7.6参与根瘤调控的机制。(Wang et al., 2020)
在拟南芥中，鉴定出两个硝酸盐转运家族NRT1、NRT2，前者更名为NPF家族。NPF家族的功能已经过大量的研究，在如uniprot在线平台可以检索其家族蛋白质的功能。对于NPF家族的功能研究，主要有以下方面：NPF在结节形成、结节器官发生中起核心作用；是表皮细胞中诱导皮层细胞分裂导致结节原基形成所必需的(Rival et al., 2012)；NPF参与结瘤前识别根瘤菌的第一步(Amor B.B., 2003)；NPF在根瘤与苜蓿根瘤菌共生期间需要通过触发感染线并将细菌释放到发育中的根瘤感染区的细胞质中(Moling et al., 2014)。
在拟南芥、水稻、玉米等作物中发现了大量的NPF家族基因，它们在硝酸盐吸收上都发挥着类似功能，这也为我们提供了研究基因功能的思路，先寻找同源基因的功能并基于此猜测和验证基因功能。
六、参考文献
Amor B.B., S. S. L., Oldroyd G.E.D., Maillet F., Penmetsa R.V., Cook D., Long S.R., Denarie J., Gough C. (2003). The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation. the plant journal, 34(4), 495-506.
Moling, S., Pietraszewska-Bogiel, A., Postma, M., Fedorova, E., Hink, M. A., Limpens, E., . . . Bisseling, T. (2014). Nod factor receptors form heteromeric complexes and are essential for intracellular infection in medicago nodules. Plant Cell, 26(10), 4188-4199. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/25351493. doi:10.1105/tpc.114.129502
Rival, P., de Billy, F., Bono, J. J., Gough, C., Rosenberg, C., & Bensmihen, S. (2012). Epidermal and cortical roles of NFP and DMI3 in coordinating early steps of nodulation in Medicago truncatula. Development, 139(18), 3383-3391. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/22874912. doi:10.1242/dev.081620
Wang, Q., Huang, Y., Ren, Z., Zhang, X., Ren, J., Su, J., . . . Kong, Z. (2020). Transfer cells mediate nitrate uptake to control root nodule symbiosis. Nat Plants, 6(7), 800-808. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/32514144. doi:10.1038/s41477-020-0683-6
