plot_pseudotime_expression_panel: Plot pseudotime expression panel
In MyersGroup/testisAtlas: testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq
Description
Usage
Arguments
Value
Description
Plot pseudotime expression panel
Usage
1
2
3
plot_pseudotime_expression_panel(genes, factorisation = SDAresults,
cell_metadata = cell_data, ncol = 7, title = "Histone Genes",
gam_k = 5, point_size = 0.2, highlight_reigon = NULL)
Arguments
genes
character vector; vector of gene symbols, of which expression values will be plotted over pseudotime
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.
ncol
numeric; number of columns to use for faceting
title
string; Title to be used in plot
gam_k
numeric; passed to gam formula, controls smoothing
point_size
numeric; size of each cell (point) in plot
highlight_reigon
numeric vector; vector of size two with min and max pseudotime values between which to highlight in the plot
Value
ggplot2 object
MyersGroup/testisAtlas documentation built on Nov. 29, 2020, 9:21 p.m.
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Description Usage Arguments Value
Description
Plot pseudotime expression panel
Usage
1 2 3 | plot_pseudotime_expression_panel(genes, factorisation = SDAresults,
cell_metadata = cell_data, ncol = 7, title = "Histone Genes",
gam_k = 5, point_size = 0.2, highlight_reigon = NULL)
|
Arguments
genes |
character vector; vector of gene symbols, of which expression values will be plotted over pseudotime |
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. |
ncol |
numeric; number of columns to use for faceting |
title |
string; Title to be used in plot |
gam_k |
numeric; passed to gam formula, controls smoothing |
point_size |
numeric; size of each cell (point) in plot |
highlight_reigon |
numeric vector; vector of size two with min and max pseudotime values between which to highlight in the plot |
Value
ggplot2 object
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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