ISS_pieplot: Venn-pie chart on ISS data based on genes of interest

In mashranga/MolDia: Single cell In-Situ sequencing (ISS) data analysis

Description

Venn-pie chart on ISS data based on genes of interest

Usage

ISS_pieplot(data, gene = NULL, with_gene = NULL, without_gene = NULL,
  segmentcol = "EEEEEE", randomseed = 10, colorpalette = NULL)

Arguments

data	Input data in class MolDiaISS. Output of readISS.
gene	Gene of interest. It could be a vector of gene or a list of genes groups. Default is NULL means takes all genes in the given dataset.
with_gene	From gene of interest , select only cells only with these genes.
without_gene	From gene of interest , select only cells only without these genes.
segmentcol	Hex color code of the overlap segment.
randomseed	Ramdom seed to change color schema.
colorpalette	Default is NULL. A vector of value . Can be applicabile with selected element with gene list.

Value

The Venn-pie plot.

Number of cells having specific gene profile.

Note

Maximum 256 genes (256 color) can be ploted with this version at this moment.

Author(s)

Mohammad Tanvir Ahamed

Examples

########## Reading data
ex_data      <- readISS(file = system.file("extdata", "CellBlobs_QT_0.35.csv", package="MolDia"),
                       cellid = "CellID",centX = "centroidX", centY = "centroidY")

## Define marker gene group
marker_gene <- ex_data@gene
c_rna <- marker_gene[grepl(".C",marker_gene)] # Circular RNA
l_rna <- setdiff(marker_gene,c_rna)           # Linear RNA

## Neuronal marker
Pyramidal   <- c("Nrn1.L","Pcp4.L")
Interneuron <- c("Sst.L","Pvalb.L","Ndnf.L","Vip.L","Sncg.L","Cck.L")
Other       <- c("Map2.L")
Neuron      <- c(Pyramidal,Interneuron,Other)

## Non-Neuronal marker
Oligodendrocyte <- c("Plp1.L","Enpp2.L")
Astrocytes  <- c("Gfap.L","Mfge8.L","Aldh1l1.L","S100b.L")
Nonneuron   <- c(Oligodendrocyte,Astrocytes)
marker_gene1 <- list(Neuron = Neuron,
                     Nonneuron = Nonneuron,
                     Cir_rna = c_rna,
                     Lin_rna = c(setdiff(setdiff(l_rna,Neuron),Nonneuron)))

####  Select cell with at least 3 neuronal genes
mydata <- ISS_barplot(data = ex_data, gene = marker_gene1, gene.target = 1,
                      at.least.gene = 3, show.same.gene = FALSE)

#####  Pie chart of all Circular mRNA in cell with at least 3 neuronal genes.
genes <- marker_gene1[[1]]
res   <- ISS_pieplot (data = mydata, gene = genes, without_gene = "QKI.L", segmentcol = "EEEEEE")

mashranga/MolDia documentation built on May 26, 2019, 9:36 a.m.