RunScatter plot
Usage
plot_runscatter(
data,
y_var,
feature_filter,
filter_exclude = FALSE,
cap_values,
cap_SPL_SD = 4,
cap_QC_SD = 4,
cap_top_n = 10,
QC_TYPE_fit = "TQC",
show_driftcorrection = FALSE,
trend_samples_fun = "loess",
trend_samples_col = "",
after_correction = FALSE,
plot_other_qc = TRUE,
show_batches = FALSE,
batches_as_shades = TRUE,
batch_line_color = "red1",
batch_shading_color = "grey85",
outputPDF,
filename = "",
cols_page = 4,
rows_page = 3,
annot_scale = 1,
paper_orientation = "LANDSCAPE",
point_transparency = 1,
point_size = 2,
point_stroke_width = 0.8,
page_no = NA,
y_label_text = NA,
silent = FALSE,
return_plot_list = FALSE,
base_size = 7
)Arguments
- data
MidarExperiment object
- y_var
Variable to plot
- feature_filter
Filter features containing
- filter_exclude
Exclude or include feature_filter
- cap_values
Cap y axis to ignore outliers
- cap_SPL_SD
Minimum s.d. of samples
- cap_QC_SD
Minimum s.d. of QCs
- cap_top_n
Cap top n values
- QC_TYPE_fit
QC TYPE used for loess fit
- show_driftcorrection
Show drift correction
- trend_samples_fun
Function used for drift correction. Default 'loess'
- trend_samples_col
Color of drift line
- after_correction
Show before/after correction
- plot_other_qc
Plot all QCS
- show_batches
Show batches
- batches_as_shades
Show batches as shades
- batch_line_color
batch separator color
- batch_shading_color
batch shade color
- outputPDF
save as PDF
- filename
file name of PDF
- cols_page
columns per page
- rows_page
rows per page
- annot_scale
scale factor of text elements
- paper_orientation
Landscape/Portrait
- point_transparency
Alpha of points
- point_size
point size
- point_stroke_width
point stroke width
- page_no
Show page number
- y_label_text
Overwrite y label with this text
- silent
Verbose or silent
- return_plot_list
return list with plots
- base_size
base font size of plot