rifi_visualization: =========================================================================...

In CyanolabFreiburg/rifi: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

========================================================================= rifi_visualization

rifi_visualization plots all the data with fragments and events from both strands

Description

rifi_visualization plots the whole genome with genes, transcription units (TUs), delay, half-life (HL), intensity fragments, features, events, velocity, annotation, coverage if available.

Usage

rifi_visualization(
  data,
  genomeLength,
  annot,
  coverage = 0,
  chr_fwd = NA,
  chr_rev = NA,
  region = c("CDS", "asRNA", "5'UTR", "ncRNA", "3'UTR", "tRNA"),
  color_region = c("grey0", "red", "blue", "orange", "yellow", "green", "white",
    "darkseagreen1", "grey50", "black"),
  color_text.1 = "grey0",
  color_text.2 = "black",
  color_TU = "blue",
  Alpha = 0.5,
  size_tu = 1.6,
  size_locusTag = 1.6,
  size_gene = 1.6,
  Limit = 10,
  shape = 22,
  col_outiler = "grey50",
  col_coverage = "grey",
  shape_outlier = 13,
  limit_intensity = NA,
  face = "bold",
  tick_length = 0.3,
  arrow.color = "darkseagreen1",
  minVelocity = 3000,
  medianVelocity = 6000,
  col_above20 = "#00FFFF",
  fontface = "plain",
  shape_above20 = 14,
  col_outlierabove10 = "darkorchid",
  shape_outlierabove10 = 5,
  axis_text_y_size = 3,
  axis_title_y_size = 6,
  TI_threshold = 1.1,
  termination_threshold = -0.5,
  iTSS_threshold = 0.5,
  p_value_int = 0.05,
  p_value_event = 0.05,
  p_value_hl = 0.05,
  p_value_TI = 0.05,
  p_value_manova = 0.05,
  event_duration_ps = 1,
  event_duration_itss = -1,
  HL_threshold_1 = log2(1.5),
  HL_threshold_2 = -log2(1.5),
  vel_threshold = 200,
  HL_threshold_color = "black",
  vel_threshold_color = "grey52",
  ps_color = "orange",
  iTSS_I_color = "blue"
)

Arguments

data	SummarizedExperiment: the input data frame with correct format.
genomeLength	integer: genome length output of gff3_preprocess function and element of metadata of SummarizedExperiment.
annot	dataframe: the annotation file, output of gff3_preprocess function and element of metadata of SummarizedExperiment.
coverage	integer: in case the coverage is available.
chr_fwd	string object: coverage of the forward strand.
chr_rev	string object: coverage of the reverse strand.
region	dataframe: gff3 features of the genome.
color_region	string vector: vector of colors.
color_text.1	string: TU color text
color_text.2	string: genes color text
color_TU	string. TU color
Alpha	integer: color transparency degree.
size_tu	integer: TU size
size_locusTag	integer: locus_tag size
size_gene	integer: font size for gene annotation.
Limit	integer: value for y-axis limit.
shape	integer: value for shape.
col_outiler	string: outlier color.
col_coverage	integer: color for coverage plot.
shape_outlier	integer: value for outlier shape.
limit_intensity	integer: intensity limit if applicable.
face	string: label font.
tick_length	integer: value for ticks.
arrow.color	string: arrows color.
minVelocity	integer: threshold to fix the minimum of velocity.
medianVelocity	integer: threshold to fix the maximum of velocity.
col_above20	string: color for probes/bin above value 20.
fontface	integer: font type
shape_above20	integer: shape for probes/bins above value 20.
col_outlierabove10	string: color for probes/bin outliers between 10 and 20,
shape_outlierabove10	integer: shape for probes/bin outliers between 10 and 20,
axis_text_y_size	integer: text size for y-axis.
axis_title_y_size	integer: title size for y-axis.
TI_threshold	integer: threshold for TI between two fragments in case the TI termination factor drops from the first segment to the second, default 1.1. If threshold is reached a line is drawn to seperates the two TI segments.
termination_threshold	integer: threshold for termination to plot, default .8.
iTSS_threshold	integer: threshold for iTSS_II selected to plot, default 1.2.
p_value_int	integer: p_value of intensity fragments fold-change to plot, default 0.05.
p_value_event	integer: p_value of t-test from pausing site and iTSS_I events to plot, default 0.05.
p_value_hl	integer: p_value of half_life fragments fold-change to plot, default 0.05.
p_value_TI	integer: p_value of TI fragments selected to be plotted, default 0.05.
p_value_manova	integer: p_value of manova test fragments to plot, default 0.05.
event_duration_ps	integer: threshold for pausing sites selected to plot, default -2.
event_duration_itss	integer: threshold for iTSS_I selected to plot, default 2.
HL_threshold_1	integer: threshold for log2FC(HL) selected to plot, default log2(1.5). log2FC(HL) >= log2(1.5) are indicated by black color. If p_value <= p_value_hl (default 0.05), log2FC(HL) is indicated by HL* otherwise HL.
HL_threshold_2	integer: threshold for log2FC(HL) selected to plot, default -log2(1.5). log2FC(HL) <= -log2(1.5) are indicated by green color. If p_value <= p_value_hl (default 0.05), log2FC(HL) is indicated by HL* otherwise HL. In case of p_value is significant and the log2FC(HL) is between -log2FC(1.5) and log2FC(1.5), FC is assigned by green color and HL*.
vel_threshold	integer: threshold for velocity ratio selected to plot, default 200.
HL_threshold_color	string: color for HL fold change plot.
vel_threshold_color	string: color for velocity ratio plot.
ps_color	string: color for pausing site plot.
iTSS_I_color	string: color for iTSS_I plot.

Details

rifi_visualization uses several functions to plot the genes including as-RNA and ncRNA and TUs as segments. The function plots delay, HL and intensity fragments with statistical t-test between the neighboring fragment, significant t-test is assigned with ''. t-test and Manova statistical test are also depicted as ''.

The functions used are:

1. annotation_plot: plots the corresponding annotation.

2. positive_strand_function: plots delay, HL, intensity and events of positive strand.

3. negative_strand_function: plots delay, HL, intensity and events of negative strand.

4. empty_data_positive: plots empty boxes in case no data is available for positive strand.

5. empty_data_negative: plots empty boxes in case no data is available for negative strand.

6. strand_selection: check if data is stranded and arrange by position.

7. splitGenome_function: splits the genome into fragments.

8. indice_function: assign a new column to the data to distinguish between fragments, outliers from delay or HL or intensity.

9. TU_annotation: designs the segments border for the genes and TUs annotation

10. gene_annot_function: it requires gff3 file, returns a dataframe adjusting each fragment according to its annotation. It allows as well the plot of genes and TUs shared into two pages.

11. label_log2_function: used to add log scale to intensity values.

12. label_square_function: used to add square scale to coverage values.

13. coverage_function: this function is used only in case of coverage is available.

14. secondaryAxis: adjusts the half-life or delay to 20 in case of the dataframe row numbers is equal to 1 and the half-life or delay exceed the limit, they are plotted with different shape and color.

15. outlier_plot: plot the outliers with half-life between 10 and 30 on the maximum of the yaxis.

16. add_genomeBorders: when the annotated genes are on the borders, they can not be plotted, therefore the region was split in 2 adding the row corresponding to the split part to the next annotation (i + 1) except for the first page.

17. my_arrow: creates an arrow for the annotation.

18. arrange_byGroup: selects the last row for each segment and add 40 nucleotides in case of negative strand for a nice plot.

19. regr: plots the predicted delay from linear regression if the data is on negative strand.

20. meanPosition: assign a mean position for the plot.

21. delay_mean: adds a column in case of velocity is NA or equal to 60. The mean of the delay is calculated outliers.

22. my_segment_T: plots terminals and pausing sites labels.

23. my_segment_NS: plots internal starting sites 'iTSS'.

24. min_value: returns minimum value for event plots in intensity plot.

25. velocity_fun: function for velocity plot.

26. limit_function: for values above 10 or 20 in delay and hl. Limit of the axis is set differently. y-axis limit is applied only if we have more than 3 values above 10 and lower or equal to 20. An exception is added in case a dataframe has less than 3 rows and 1 or more values are above 10, the rest of the values above 20 are adjusted to 20 on "secondaryAxis" function.

27. empty_boxes: used only in case the dataframe from the positive strand is not empty, the TU are annotated.

28. function_TU_arrow: used to avoid plotting arrows when a TU is split into two pages.

29. terminal_plot_lm: draws a linear regression line when terminal outliers have an intensity above a certain threshold and are consecutive. Usually are smallRNA (ncRNA, asRNA).

30. slope_function: replaces slope lower than 0.0009 to 0.

31. velo_function: replaces infinite velocity with NA.

32. plot the coverage of RNA_seq in exponential phase growth

Value

The visualization plot.

Examples

data(stats_minimal)
if(!require(SummarizedExperiment)){
suppressPackageStartupMessages(library(SummarizedExperiment))
}
rifi_visualization(data = stats_minimal, 
genomeLength = metadata(stats_minimal)$annot[[2]],
annot = metadata(stats_minimal)$annot[[1]])

CyanolabFreiburg/rifi documentation built on May 7, 2023, 7:53 p.m.