michaelgruenstaeudl
commented
4 months ago All completed.
Closed michaelgruenstaeudl closed 4 months ago
michaelgruenstaeudl
commented
4 months ago All completed.
[x] Length standardization of WRSD (relevant for Figure 2, Tables 2-4) Rather than a length normalization (i.e., values between 0 and 1), we should try to achieve a length standardization in which the number of WRSD is standardized but not near zero. I tried to explain my idea here: https://stats.stackexchange.com/questions/647644/standardization-of-summary-statistic-of-group-linked-values
[x] Removal of outliers in Figure 2 Once the above-mentioned standardization is achieved and we still see as many outlier values of WRSD as we currently do in Figure 2, we should try to remove these outliers from both the visualization and the statistical tests.
[x] Value exactness in Table 2 It is sufficient to give only two places after the comma in the line "E-score" of Table 2. Otherwise the reader believes that we want to point out some minute value changes to him, which we don't for that line. Similarly, only one place after the comma is sufficient for mean and SD in lines "Ambiguous nucl." and "IR mismatches".
[x] Wrong position of red labels in Figure 1A Many of the accession number labels of Figure 1A (i.e., the labels in red) are not in the vicinity of the dots they are labeling. This is especially dramatic for the label of NC_026562, which is references in the text and the figure caption but nowhere near the underlying dot in the figure. Once all other code adjustments have been achieved, it may be necessary to align the red labels by hand.
[x] Include subplot labels in Figure 1 Include subplot labels in Figure 1A and Figure 1B, respectively
[x] Not related to figures but still relevant Can you please help me complete the sentences of the introduction section of our manuscript: "Sequencing evenness can also been measured through a separate evenness score ('E-score'; Mokry et al. 2010), which calculates ..."
[x] Special calculation necessary for manuscript For subsection 'Sequencing depth and coding status' of the Discussion section, I would need to know the cumulative length of all coding regions (i.e., genes) and the cumulative length of all non-coding regions per genome. I would then average this ratio across all 194 plastid genomes under study to obtain the relevant number for this manuscript subsection. Could you update PACVr so that this cumulative length information is written into the output of each genome as well?
[x] Vertical positioning of supplemental figures I had to split the supplemental materials containing the supplemental figures into two separate files, as the file size would otherwise have exceeded 20 MB (i.e., the limit of most journals for individual files). Weirdly, some of the supplemental figures are arranged on the top of the page, some - as they should - in the center of the page. If you have time, maybe you can take a look at it and have them all vertically centered.
[x] Arranging subplots of Figure 1 vertically, not horizontally To improve the legibility of Figure 1, can you please arranged its two subplots vertically. That way, each subplot will be larger and better readable.