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) # }