Description Usage Arguments Value References Examples
Generates a cylindrical grid of the appropriate dimensions for a 3D volcano plot
1 2 3 4 5 6 7 8 9 |
r_vector |
An optional numerical vector for the radial coordinates.
This is used to calculate breaks on the r axis using
|
z_vector |
An optional numerical vector for the z coordinates.
This is used to calculate breaks on the z axis using |
r_axis_ticks |
A numerical vector of breaks for the radial axis (used if r_vector is NULL). |
z_axis_ticks |
A numerical vector of breaks for the z axis (used if z_vector is NULL). |
axis_angle |
angle in radians to position the radial axis (default = 5/6) |
n_spokes |
the number of outward spokes to be plotted (default = 12) |
... |
optional parameters for |
Returns an S4 grid object containing:
'polar_grid' The coordinates for a radial grid
'axes' The axes features for 'plotly'
'axis_labels' The axis labels
'r' The grid radius
'z' The grid height
'text_coords' The coordinates for text labels
'n_r_breaks' The number of ticks on the r axis
'n_r_breaks' The number of ticks on the z axis
Lewis, Myles J., et al. (2019). Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell reports, 28:9
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | data(example_data)
syn_polar <- polar_coords(sampledata = syn_example_meta,
contrast = "Pathotype",
groups = NULL,
pvalues = syn_example_p,
expression = syn_example_rld,
p_col_suffix = "pvalue",
padj_col_suffix = "padj",
non_sig_name = "Not Significant",
multi_group_prefix = "LRT",
significance_cutoff = 0.01,
fc_col_suffix='log2FoldChange',
fc_cutoff = 0.3)
grid <- polar_grid(r_vector=syn_polar@polar$r_zscore,
z_vector=NULL,
r_axis_ticks = NULL,
z_axis_ticks = c(0, 8, 16, 32),
n_spokes = 4)
|
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