## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
library(nMyo)
## ----loading------------------------------------------------------------------
data(nMyo_Data)
data<-readData(nMyo_Data,Markers_file=NULL,is.Exact=TRUE,logFC_cutoff=0,FDR_cutoff=1)
# listed components
names(data)
# the CorrCounts
data$Counts[1:5, 1:5]
# the design_table
data$Design[1:5, ]
# the DE
data$DEstats[1:5, ]
# the data stamp (for file storage)
data$Date_Stamp
## ----query1-------------------------------------------------------------------
data_Postn <- MarkerQuery(Data = data, marker = "Postn")
## ----query2-------------------------------------------------------------------
data_Postn_alt <- MarkerQuery(Data = data, marker = "ENSMUSG00000027750")
## ----query3-------------------------------------------------------------------
data_Postn_alt2 <- MarkerQuery(Data = data, marker = "ENSMUSG00000027750:Postn")
## ----query4-------------------------------------------------------------------
data_Postn_err <- MarkerQuery(Data = data, marker = "Post")
## ----query5-------------------------------------------------------------------
data_err <- MarkerQuery(Data = data, marker = "Tp53")
## ----tsne---------------------------------------------------------------------
scatter_Postn <- doScatterDR(Data = data_Postn,
highlight.by = "CellType",
show.plot = TRUE,
save.plot = FALSE)
## ----violin-------------------------------------------------------------------
violin_Postn <- doViolin(Data = data_Postn,
grouping.by = "CellType",
grouping2.by = "Condition",
show.plot = TRUE,
save.plot = FALSE)
## ----violin2------------------------------------------------------------------
violin_Postn2 <- doViolin(Data = data_Postn,
grouping.by = "CellType",
grouping2.by = "",
show.plot = TRUE,
save.plot = FALSE)
## ----volcano------------------------------------------------------------------
volcano_Postn <- doVolcano(Data = data_Postn,
filters = "Comparison=='Fibroblast: Sham-MI'",
logFC = 1,
FDR = 0.01,
show.plot = TRUE,
save.plot = FALSE)
## ----pairwise-----------------------------------------------------------------
# all pairwise comparisons (to be used in filter parameter)
names(table(data$DEstats$Comparison))
## ----ma-----------------------------------------------------------------------
ma_Postn <- doMA(Data = data_Postn,
filters = "Comparison=='Fibroblast: Sham-MI'",
logFC = 1,
FDR = 0.01,
show.plot = TRUE,
save.plot = FALSE)
## ----run_app, eval=FALSE------------------------------------------------------
# run_nMyo()
## ----pressure, echo=FALSE, fig.cap="nMyo welcome screen", out.width = '100%'----
knitr::include_graphics("screen1.png")
## ----pressure2, echo=FALSE, fig.cap="nMyo welcome screen", out.width = '100%'----
knitr::include_graphics("screen2.png")
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