Transcriptomics_Stems_CW {WallomicsData}

Transcriptomics Stems Cell Wall

Description

A dataset containing the transcripts encoding Cell Wall Proteins (CWPs) sorted from the 22 570 transcripts (see Transcriptomics_Stems) obtained by RNA-seq performed, according to the standard Illumina protocols, on floral stems of five A. thaliana genotypes at two growth temperatures. See Ecotype and Temperature for more information.

Usage

data("Transcriptomics_Stems_CW")

Format

A data frame with 30 rows and 414 variables.

Source

doi: 10.3390/cells9102249

Examples

# Load the dataset
data("Transcriptomics_Stems_CW")

# Look at data frame dimensions
dim(Transcriptomics_Stems_CW)

# Look at the first rows and columns
head(Transcriptomics_Stems_CW[,c(1:10)])

# Create a colors' vector
colors <- c(rep("#A6CEE3",3), rep("#1F78B4",3), rep("#B2DF8A",3), rep("#33A02C",3),
            rep("#FB9A99",3), rep("#E31A1C",3), rep("#FDBF6F",3), rep("#FF7F00",3),
            rep("#CAB2D6",3), rep("#6A3D9A",3))

# PCA on transcriptomics
res.pca <- prcomp(Transcriptomics_Stems_CW, center = TRUE, scale. = TRUE)
plot(res.pca$x[,"PC1"], res.pca$x[,"PC2"], pch = 19, xlab = "PC1", ylab = "PC2", lwd = 5,
     main = "Individuals' plot (1 x 2) - PCA on Stems Cell Wall Transcriptomics",
     col = colors)
text(res.pca$x[,"PC1"], res.pca$x[,"PC2"], labels = row.names(res.pca$x), cex = 0.8, pos = 3)