View source: R/facs_density_plot2.R
facs_density_plot2 | R Documentation |
Given a path to a directory containing .fcs
files and a pattern to
match in the file names, generates density plots of FACS data across time
points.
facs_density_plot2( strain_code, dir = "./", output_dir = dir, gate, y_axis_label = "Time in meiosis\n(hrs)\n", plot_color = "black", plot_transparency = 0.8, file_format = "jpeg", user_input = TRUE )
strain_code |
The lab's database numeric code identifier of the yeast strain (used to name files). No default. |
dir |
Path to directory containing |
output_dir |
Path to output directory. Defaults to |
gate |
Optional two-element vector containing gating limits. No default (corresponds to no gating). |
y_axis_label |
Character string indicating the label for the plot's y
axis. Defaults to |
plot_color |
Optional R color to fill the plot. Defaults to
|
plot_transparency |
Floating point number between 0 and 1 indicating
transparency of the plot (corresponds to the plotting |
file_format |
Character string indicating the plot file format. Must be
one of the options |
user_input |
Logical indicating whether to ask user before saving plot
to file. Defaults to |
Density plot file in the same directory as the .fcs
files.
The function is designed to search all .fcs
files (named according to
the convention "Well strain_timepoint.fcs". e.g. "A01 119_0.fcs") for those
matching the provided pattern (yeast strain code) and build a density plot.
An ungated version of the plot is printed to the screen and the final plot is
saved to a file in the selected format in the same directory as the
.fcs
files.
## Not run: facs_density_plot2(119) facs_density_plot2(strain_code=8401, dir='~/Desktop/my_facs_data', output_dir='~/Desktop', gate=c(1500000, 7000000)) facs_density_plot2(strain_code=119, dir='~/Desktop/', output_dir='~/Desktop', gate=c(1500000, 7000000), y_axis_label='Samples', plot_color='orange', plot_transparency=1, user_input=F) ## End(Not run)
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