print_tsne: Plot tSNE

In MyersGroup/testisAtlas: testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq

Description

Plot tSNE

Usage

print_tsne(i, factorisation = SDAresults, cell_metadata = cell_data,
  jitter = 0, colourscale = "diverging", expression_matrix = data,
  princurves = principal_curves, dim1 = "Tsne1_QC1",
  dim2 = "Tsne2_QC1", flip = FALSE, predict = FALSE, curve = FALSE,
  stages = FALSE, point_size = 1, log = FALSE,
  principal_curve = "df_9", curve_width = 0.5)

Arguments

i	; either a numeric value corresponding to the component to plot, a gene name, or the name of a variable stored in cell_data such as "group", "PseudoTime", or "library_size"
factorisation	SDA factorisation object, output of SDAtools::load_results()
cell_metadata	data.table with columns cell, Tsne1_QC1, Tsne2_QC2, and components V1, V2 etc.
expression_matrix	cell by gene matrix of expression values
princurves	list of outputs of princurve()
dim1	string; name of variable in cell_metadata of the x axis to be used for the plot
dim2	string; name of variable in cell_metadata of the y axis to be used for the plot
flip	logical; should the cell scores be multiplied by -1 (score/gene loading sign combination are arbitrary like PCA scores).
predict	logical; Should gene expression be the predicted (imputed) values or raw normalised
curve	logical; Should principal curve (pseudotime) by plotted on top of the tSNE plot
stages	logical; Should the stages be annotated
point_size	numeric; size of point
log	logical; should the varible mapped to the colour of the points be log transformed, default: F
principal_curve	string; name of list entry in principal_curves object, to use for pseudotime line
curve_width	numeric; width of the pseudotime curve

Details

will add titles if you run load_component_orderings()

Value

The Y matrix from Rtsne output, rotated by angle

MyersGroup/testisAtlas documentation built on Nov. 29, 2020, 9:21 p.m.