Description Usage Arguments Value References Examples
Plots the pvalues from three-way comparisons in 3D space using plotly.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | volcano3D(
polar,
colours = c("green3", "cyan", "blue", "purple", "red", "gold2"),
non_sig_colour = "grey60",
colour_scale = "discrete",
continuous_shift = 1.33,
label_rows = c(),
grid = NULL,
fc_or_zscore = "zscore",
label_size = 14,
arrow_length = 50,
colour_code_labels = TRUE,
label_colour = NULL,
grid_colour = "grey80",
axis_colour = "black",
marker_size = 2.7,
marker_alpha = 1,
marker_outline_colour = "white",
marker_outline_width = 0,
axis_angle = 0.5,
z_aspectratio = 1,
xy_aspectratio = 1,
plot_height = 700,
...
)
|
polar |
A polar object with created by |
colours |
A vector of colour names or hex triplets for each of the six groups. Default = c("green3", "cyan", "blue", "purple", "red", "gold2"). Colours are assigned in order: group1+, group1+group2+, group2+, group2+group3+, group3+, group1+group3+. |
non_sig_colour |
The colour for non-significant markers (default='grey60'). |
colour_scale |
whether to use a 'discrete' or 'continuous' colour scale (default = 'discrete'). |
continuous_shift |
The number of radians
to offset the continuous colour scale by. This is calculated by converting
the angle to a hue using |
label_rows |
A vector of row names or numbers to label. |
grid |
An optional grid object. If NULL this will be calculated using
default values of |
fc_or_zscore |
whether to use fold change or z-score for the p-values. Options are 'zscore' (default) or 'fc'). |
label_size |
font size for labels (default = 14). |
arrow_length |
The length of label arrows (default = 50). |
colour_code_labels |
Logical whether label annotations should be colour coded. If FALSE label_colour is used. |
label_colour |
HTML colour of annotation labels if not colour coded. |
grid_colour |
The colour of the cylindrical grid (default="grey80"). |
axis_colour |
The colour of the grid axes and labels (default="black"). |
marker_size |
Size of the markers (default = 2.7). |
marker_alpha |
Opacity for the markers (default = 1). |
marker_outline_colour |
Colour for marker outline (default = white) |
marker_outline_width |
Width for marker outline (default = 0) |
axis_angle |
Angle in radians for the z axis (default = 0.5). |
z_aspectratio |
The aspect ratio for the z axis compared to x and y (default = 1). Decreasing this makes the plot appear more squat. |
xy_aspectratio |
The aspect ratio for the xy axis compared to z (default = 1). Decreasing this makes the grid wider in the plot window. |
plot_height |
The plot height in px. Default=700. |
... |
Optional parameters to pass to |
Returns a cylindrical 3D plotly plot featuring variables on a tri-axis radial graph with the -log10(multi-group test p-value) 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)
volcano3D(syn_polar,
label_rows = c("FMOD", "LAMP5", "TNNT3"),
xy_aspectratio = 1,
label_size = 10,
z_aspectratio = 0.9)
|
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